From 5eb028e1c6f802ec830338f3ab199cb7b338eec1 Mon Sep 17 00:00:00 2001
From: Nichole <55827494+nicholema@users.noreply.github.com>
Date: Tue, 23 Jul 2024 19:00:02 +0000
Subject: [PATCH] add AP field in mergeSTR hipstr output

---
 trtools/mergeSTR/mergeSTR.py                  |    2 +-
 trtools/mergeSTR/tests/test_mergeSTR.py       |   14 +
 .../beagle/hipstr_imputed_merge1.vcf          | 3416 +++++++++++++++++
 .../beagle/hipstr_imputed_merge2.vcf          | 3416 +++++++++++++++++
 .../hipstr_imputed_merge1.vcf.gz              |  Bin 0 -> 30083 bytes
 .../hipstr_imputed_merge1.vcf.gz.tbi          |  Bin 0 -> 130 bytes
 .../hipstr_imputed_merge2.vcf.gz              |  Bin 0 -> 30088 bytes
 .../hipstr_imputed_merge2.vcf.gz.tbi          |  Bin 0 -> 130 bytes
 8 files changed, 6847 insertions(+), 1 deletion(-)
 create mode 100644 trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge1.vcf
 create mode 100644 trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge2.vcf
 create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz
 create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz.tbi
 create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz
 create mode 100644 trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz.tbi

diff --git a/trtools/mergeSTR/mergeSTR.py b/trtools/mergeSTR/mergeSTR.py
index 2fb3d96a..62d9571e 100644
--- a/trtools/mergeSTR/mergeSTR.py
+++ b/trtools/mergeSTR/mergeSTR.py
@@ -45,7 +45,7 @@
 FORMATFIELDS = {
     trh.VcfTypes.gangstr: ["DP", "Q", "REPCN", "REPCI", "RC", "ENCLREADS", "FLNKREADS", "ML", "INS", "STDERR", "QEXP"],
     trh.VcfTypes.hipstr: ["GB", "Q", "PQ", "DP", "DSNP", "PSNP", "PDP", "GLDIFF", "DSTUTTER", "DFLANKINDEL", "AB", "FS",
-                          "DAB", "ALLREADS", "MALLREADS","AP1","AP2"],
+                          "DAB", "ALLREADS", "MALLREADS","AP1","AP2","DS"],
     trh.VcfTypes.eh: ["ADFL", "ADIR", "ADSP", "LC", "REPCI", "REPCN", "SO"],
     trh.VcfTypes.popstr: ["AD", "DP", "PL"],
     trh.VcfTypes.advntr: ["DP", "SR", "FR", "ML"]
diff --git a/trtools/mergeSTR/tests/test_mergeSTR.py b/trtools/mergeSTR/tests/test_mergeSTR.py
index 0662339b..3fb44ee0 100644
--- a/trtools/mergeSTR/tests/test_mergeSTR.py
+++ b/trtools/mergeSTR/tests/test_mergeSTR.py
@@ -115,6 +115,20 @@ def test_hipSTRRightFile(args, mrgvcfdir):
     args.verbose = True
     assert main(args)==0
 
+# Test right files or directory - hipstr with FORMAT field
+def test_hipSTRRightFile_AP(args, mrgvcfdir):
+    fname1 = os.path.join(mrgvcfdir, "hipstr_imputed_merge1.vcf.gz")
+    fname2 = os.path.join(mrgvcfdir, "hipstr_imputed_merge2.vcf.gz")
+    args.vcftype = "hipstr"
+    args.vcfs = fname1 + "," + fname2
+    assert main(args)==0
+    args.vcftype = "auto"
+    assert main(args)==0
+    args.update_sample_from_file = True
+    assert main(args)==0
+    args.verbose = True
+    assert main(args)==0
+
 # Test right files or directory - ExpansionHunter
 def test_ExpansionHunterRightFile(args, mrgvcfdir):
     fname1 = os.path.join(mrgvcfdir, "test_file_eh1.vcf.gz")
diff --git a/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge1.vcf b/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge1.vcf
new file mode 100644
index 00000000..2f4a8cf0
--- /dev/null
+++ b/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge1.vcf
@@ -0,0 +1,3416 @@
+##fileformat=VCFv4.2
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/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01882.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01883.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01885.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01956.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02014.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01886.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01890.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01889.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02009.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02010.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01914.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01915.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01986.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01958.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01990.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02012.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02053.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02054.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02255.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02256.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02314.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02315.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02281.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02282.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02317.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02318.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01912.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01894.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01879.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01880.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02013.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01896.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01985.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01988.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01989.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02051.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02052.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02095.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02332.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02108.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02111.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02143.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02307.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02308.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02283.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02309.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02284.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02322.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02323.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02325.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02337.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02330.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02339.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02343.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02419.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02420.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02427.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02429.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02433.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02442.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02445.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02489.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02449.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02450.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02470.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02471.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02479.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02484.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02485.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02511.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02496.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02497.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02508.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02537.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02439.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02455.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02476.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02477.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02481.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02501.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02502.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02505.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02536.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02541.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02545.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02546.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02549.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02554.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02555.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02557.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02558.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02577.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02580.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01884.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01887.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01888.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01891.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01895.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01897.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01916.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01959.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01960.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01987.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02011.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02055.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02145.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02257.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02258.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02280.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02316.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02321.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02451.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ACB/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ACB/splits/00/running_out/ACB_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19625.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19700.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19701.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19703.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19704.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19707.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19711.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19712.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19713.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19818.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19819.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19834.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19835.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19900.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19901.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19904.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19908.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19909.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19914.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19916.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19920.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19921.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19982.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20126.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20276.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20278.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20281.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20282.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20287.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20289.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20291.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20294.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20296.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20299.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20314.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20317.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20332.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20340.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20342.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20346.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20348.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20356.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20357.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20359.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19922.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19923.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19984.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20298.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20339.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20351.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20412.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19913.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20274.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20318.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20320.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20321.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20355.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20362.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19702.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19705.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19828.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19836.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19902.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19918.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19919.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19924.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19983.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA20128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA20129.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA20279.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA20358.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ASW/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ASW/splits/00/running_out/ASW_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03007.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03615.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03616.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03793.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03796.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03800.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03803.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03802.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03815.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03814.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03824.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03823.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03826.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03830.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03829.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03833.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03832.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03914.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03913.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03941.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03940.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04155.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04156.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03607.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03805.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03908.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03907.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03926.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03925.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03594.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03595.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03809.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03808.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03009.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03812.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03817.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03902.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03012.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03905.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03911.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03910.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03916.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03919.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03928.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03931.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03585.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03937.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03934.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03589.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04159.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03593.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04186.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03598.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04158.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04185.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04131.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04134.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04140.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04173.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04182.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04183.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03821.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03922.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04180.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03600.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03603.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03604.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03611.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03920.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04152.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04153.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04161.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04162.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04164.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04171.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04176.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04177.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04188.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04189.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04194.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04195.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03008.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03596.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03605.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03606.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03617.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03794.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03795.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03797.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03798.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03799.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03801.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03804.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03806.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03807.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03816.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03825.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03831.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03834.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03904.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03906.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03909.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03915.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03927.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03929.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03930.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03942.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04132.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04133.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04135.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04136.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04147.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04148.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04149.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04150.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04151.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04157.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04160.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04174.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04175.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04184.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04187.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04191.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04192.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04193.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/BEB/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/BEB/splits/00/running_out/BEB_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00759.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00766.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00844.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00879.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00956.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00978.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00982.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01028.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01029.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01031.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01046.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01794.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01795.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01796.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01797.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01798.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01799.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01800.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01801.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01802.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01804.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01805.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01806.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01807.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01808.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01809.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01810.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01811.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01812.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01813.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02151.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01815.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01816.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01817.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02152.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02153.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02154.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02155.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02156.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02164.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02165.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02166.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02178.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02179.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02180.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02181.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02182.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02184.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02185.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02186.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02187.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02188.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02190.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02373.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02394.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02396.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02397.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02250.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02351.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02353.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02355.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02356.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02360.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02364.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02367.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02371.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02374.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02375.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02379.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02380.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02382.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02383.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02384.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02385.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02386.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02389.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02390.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02391.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02392.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02395.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02398.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02399.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02401.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02402.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02406.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02407.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02409.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02408.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02410.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CDX/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CDX/splits/00/running_out/CDX_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06985.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06986.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06994.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07000.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07037.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07051.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07347.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07357.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA10847.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA10851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11829.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11830.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11831.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11832.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11840.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11894.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11918.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11919.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11920.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11931.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11992.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11994.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11995.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12003.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12004.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12005.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12043.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12044.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12045.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12154.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12155.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12156.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12234.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12249.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12287.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12414.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12489.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12716.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12717.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12749.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12750.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12751.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12760.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12761.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12762.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12763.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12776.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12812.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12813.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12814.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12815.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12828.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12873.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12878.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06984.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06989.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11843.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11892.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11893.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11930.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12058.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12272.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12273.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12275.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12282.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12283.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12286.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12340.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12341.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12342.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12347.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12348.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12383.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12399.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12400.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12413.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12718.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12748.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12777.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12827.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12829.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12842.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12843.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12889.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12890.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07048.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11932.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11933.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12046.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12830.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12546.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA06991.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA06993.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA06995.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA06997.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07014.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07022.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07029.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07031.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07034.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07045.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07055.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07345.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07346.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07348.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07349.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07435.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10830.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10831.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10835.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10836.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10837.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10838.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10839.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10840.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10842.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10843.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10845.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10846.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10852.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10854.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10855.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10856.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10857.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10859.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10860.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10865.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11839.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11882.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11891.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11993.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12057.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12145.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12236.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12248.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12264.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12274.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12329.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12335.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12336.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12343.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12344.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12376.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12386.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12485.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12707.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12739.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12740.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12752.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12753.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12766.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12767.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12801.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12802.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12817.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12818.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12832.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12865.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12875.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12877.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12891.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12892.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/CEU/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/CEU/splits/00/running_out/CEU_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18526.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18532.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18537.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18542.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18545.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18547.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18550.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18552.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18555.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18558.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18561.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18562.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18563.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18564.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18566.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18570.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18571.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18572.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18573.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18577.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18579.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18582.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18592.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18593.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18603.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18605.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18608.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18609.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18638.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18614.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18530.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18534.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18536.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18543.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18544.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18546.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18548.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18549.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18557.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18559.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18595.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18596.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18597.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18599.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18602.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18606.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18610.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18611.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18612.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18613.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18615.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18616.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18617.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18618.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18619.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18620.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18621.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18622.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18623.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18624.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18625.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18626.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18627.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18628.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18630.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18631.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18632.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18633.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18634.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18635.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18636.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18637.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18639.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18640.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18641.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18642.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18643.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18645.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18647.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18740.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18745.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18747.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18748.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18749.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18757.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18525.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18528.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18531.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18533.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18535.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18538.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18539.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18541.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18553.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18560.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18565.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18567.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18574.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18591.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18629.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18644.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18646.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18648.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CHB/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CHB/splits/00/running_out/CHB_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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--fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CHS/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CHS/splits/00/running_out/CHS_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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/HG01391.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01433.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01439.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01457.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01463.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01466.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01490.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01493.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01496.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01499.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01552.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/CLM/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/CLM/splits/00/running_out/CLM_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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--fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ESN/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ESN/splits/00/running_out/ESN_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00171.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00173.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00174.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00176.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00177.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00178.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00179.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00180.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00181.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00182.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00183.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00185.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00186.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00187.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00188.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00189.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00190.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00266.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00267.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00268.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00269.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00271.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00272.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00273.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00306.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00308.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00309.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00311.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00313.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00315.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00318.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00319.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00320.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00321.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00323.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00327.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00328.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00335.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00336.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00337.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00338.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00339.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00342.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00343.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00344.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00345.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00346.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00349.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00350.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00351.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00353.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00355.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00356.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00357.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00358.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00360.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00361.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00362.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00364.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00365.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00366.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00367.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00368.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00369.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00371.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00372.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00373.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00375.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00376.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00378.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00379.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00380.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00381.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00382.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00384.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00274.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00275.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00276.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00277.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00278.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00280.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00281.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00282.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00284.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00285.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00310.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00324.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00325.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00326.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00329.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00330.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00331.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00332.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00341.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00383.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00288.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00290.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00304.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/FIN/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/FIN/splits/00/running_out/FIN_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00096.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00097.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00101.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00102.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00103.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00105.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00108.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00109.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00110.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00111.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00112.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00113.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00114.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00115.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00116.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00117.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00120.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00129.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00130.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00131.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00132.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00133.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00136.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00137.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00138.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00139.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00140.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00143.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00145.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00148.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00149.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00150.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00151.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00155.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00157.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00158.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00160.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00233.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00234.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00235.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00238.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00240.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00255.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00118.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00119.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00121.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00123.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00125.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00126.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00159.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00231.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00232.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00236.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00237.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00242.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00243.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00244.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00245.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00252.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00253.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00254.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00256.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00257.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00258.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00259.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00260.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00261.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00262.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00263.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00264.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00265.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00154.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00246.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00250.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00251.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01789.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01791.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02215.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/GBR/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/GBR/splits/00/running_out/GBR_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20845.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20846.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20847.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20849.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20850.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20852.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20853.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20854.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20856.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20858.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20859.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20862.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20866.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20869.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20870.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20875.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20876.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20877.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20878.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20882.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20884.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20885.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20886.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20887.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20888.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20889.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20890.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20891.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20892.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20894.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20895.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20896.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20897.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20899.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20900.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20901.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20902.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20903.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20904.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20906.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20908.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20910.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20911.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21086.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21088.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21089.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21090.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21091.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21092.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21094.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21097.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21098.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21101.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21102.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21103.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21104.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21105.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21108.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21109.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21110.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21111.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21112.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21113.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21115.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21116.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21117.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21118.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21119.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21120.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21123.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21125.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21130.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21133.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21135.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21137.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21143.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20868.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20905.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21087.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21093.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21095.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21114.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21124.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21126.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21129.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/GIH/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/GIH/splits/00/running_out/GIH_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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1000Genomes/additional_698_related/HG03540.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/GWD/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/GWD/splits/00/running_out/GWD_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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--fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/IBS/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/IBS/splits/00/running_out/IBS_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03713.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03716.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03714.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03717.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03722.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03730.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03727.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03729.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03731.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03771.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03770.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03882.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03781.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03773.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03772.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03786.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03784.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03787.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03788.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03789.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03869.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03862.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03978.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03971.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03974.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03976.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03973.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04002.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04017.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04026.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03977.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03780.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03718.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04018.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03742.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03779.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03777.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03785.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03792.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03782.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03873.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03870.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03963.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03960.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03968.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03720.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04025.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04020.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04014.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04015.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04022.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04063.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04093.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04118.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03774.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04001.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03866.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03969.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04023.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04060.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04090.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04054.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04061.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04062.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04059.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04076.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04080.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04094.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04096.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04098.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04209.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04198.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04200.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04206.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04202.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04211.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04212.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04222.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04214.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04216.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04219.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04225.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04235.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04238.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03875.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03965.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04070.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03868.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03871.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03967.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03719.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03721.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03725.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03732.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04217.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/ITU/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/ITU/splits/00/running_out/ITU_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18940.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18942.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18943.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18944.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18945.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18947.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18948.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18949.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18951.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18952.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18953.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18956.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18959.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18960.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18961.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18964.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18965.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18967.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18968.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18969.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18970.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18971.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18972.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18973.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18974.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18975.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18976.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18980.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18981.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19005.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18939.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18941.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18946.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18954.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18957.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18962.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18963.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18966.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18977.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18978.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18979.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18987.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18990.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18991.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18992.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18993.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18994.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18995.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18997.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18998.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18999.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19000.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19001.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19002.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19003.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19007.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19009.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19010.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19012.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19054.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19055.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19057.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19058.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19059.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19060.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19062.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19063.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19064.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19065.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19066.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19067.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19068.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19070.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19072.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19074.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19075.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19076.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19077.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19078.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19079.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19080.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19081.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19082.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19083.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19084.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19085.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19086.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19087.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19088.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18950.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18982.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18983.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18984.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18985.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18986.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18988.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18989.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19004.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19011.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19089.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19090.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19091.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/JPT/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/JPT/splits/00/running_out/JPT_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02017.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02016.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02020.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02023.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02026.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02025.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02029.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02028.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02058.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02057.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02070.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02069.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02073.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02072.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02076.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02075.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02079.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02078.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02082.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02081.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02085.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02084.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02134.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02133.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01841.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01595.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01596.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01597.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01598.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01599.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01600.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01840.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01842.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01843.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01844.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01845.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01846.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01847.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01848.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01849.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01850.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01852.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01853.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01855.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01857.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01858.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01859.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01860.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01862.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01865.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01866.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01868.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01869.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01870.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01871.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01873.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01878.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02048.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02049.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02086.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02087.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02088.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02138.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02139.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02140.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02113.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02121.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02032.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02031.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02050.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02035.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02040.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02047.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02061.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02060.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02064.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02067.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02116.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02131.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02130.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02137.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02136.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02512.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02513.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02521.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02522.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02015.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02018.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02024.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02027.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02030.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02059.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02068.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02071.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02074.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02077.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02080.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02083.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02120.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02126.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02129.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02132.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02135.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02514.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02523.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02524.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02525.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02526.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/KHV/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/KHV/splits/00/running_out/KHV_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19017.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19020.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19023.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19024.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19025.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19026.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19027.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19028.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19030.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19031.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19035.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19036.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19037.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19038.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19041.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19042.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19043.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19307.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19308.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19309.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19310.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19312.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19314.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19315.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19316.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19317.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19318.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19319.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19320.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19321.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19323.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19324.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19327.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19328.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19331.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19332.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19338.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19346.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19347.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19350.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19351.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19355.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19360.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19372.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19374.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19375.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19376.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19377.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19378.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19379.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19380.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19383.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19384.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19385.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19390.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19391.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19393.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19394.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19395.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19397.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19399.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19401.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19403.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19404.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19428.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19429.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19430.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19431.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19434.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19435.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19436.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19437.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19438.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19439.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19440.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19443.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19445.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19446.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19448.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19449.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19451.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19452.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19454.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19455.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19456.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19457.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19461.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19462.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19463.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19466.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19467.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19468.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19471.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19472.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19473.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19474.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19475.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/LWK/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/LWK/splits/00/running_out/LWK_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03052.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03057.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03058.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03078.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03084.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03085.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03096.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03097.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03397.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03451.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03452.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03464.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03469.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03472.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03470.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03473.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03081.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03088.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03209.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03212.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03055.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03376.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03380.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03385.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03388.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03401.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03419.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03061.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03428.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03433.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03439.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03442.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03445.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03446.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03460.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03461.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03478.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03479.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03066.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03069.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03072.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03410.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03436.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03437.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03449.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03458.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03476.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03484.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03485.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03547.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03548.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03556.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03557.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03391.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03455.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03559.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03563.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03565.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03571.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03572.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03575.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03577.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03578.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03583.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03054.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03060.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03063.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03064.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03073.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03074.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03077.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03079.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03082.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03086.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03091.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03095.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03224.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03225.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03378.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03382.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03394.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03432.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03457.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03558.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03567.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03065.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03098.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03438.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03453.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03454.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03456.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03480.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03486.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03574.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03576.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03579.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03582.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03584.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/MSL/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/MSL/splits/00/running_out/MSL_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19648.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19649.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19651.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19652.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19654.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19655.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19657.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19658.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19661.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19663.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19664.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19669.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19670.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19676.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19678.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19679.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19681.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19682.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19684.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19716.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19717.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19719.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19720.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19722.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19723.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19725.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19726.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19728.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19729.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19731.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19732.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19746.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19747.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19749.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19750.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19755.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19756.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19758.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19759.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19761.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19762.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19770.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19771.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19773.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19774.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19776.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19777.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19779.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19780.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19782.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19783.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19785.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19786.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19788.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19789.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19794.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19795.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19734.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19735.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19740.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19741.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19752.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19764.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19792.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19650.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19653.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19656.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19659.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19660.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19662.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19665.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19671.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19675.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19677.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19680.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19683.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19685.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19686.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19718.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19721.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19724.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19727.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19730.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19733.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19748.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19751.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19757.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19760.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19763.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19772.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19781.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19784.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19787.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19796.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/MXL/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/MXL/splits/00/running_out/MXL_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01565.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01566.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01571.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01572.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01577.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01578.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01918.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01892.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01893.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01920.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01921.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01923.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01924.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01926.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01927.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01932.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01933.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01935.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01936.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01938.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01939.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01941.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01942.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01944.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01945.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01947.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01948.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01950.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01951.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01953.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01954.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01967.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01968.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01970.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01971.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01974.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01973.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01977.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01976.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01979.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01980.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01991.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01992.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02008.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01997.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02002.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02003.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02090.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02089.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02104.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02105.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02285.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02286.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02301.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01982.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02147.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02259.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02260.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02271.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02272.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02277.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02278.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02291.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02292.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02299.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02298.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01961.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01965.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02102.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02150.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02252.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02253.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02262.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02265.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02266.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02274.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02275.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02304.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02312.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02345.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02348.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02425.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01567.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01573.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01579.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01898.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01919.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01922.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01925.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01928.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01934.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01937.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01940.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01943.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01946.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01949.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01952.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01955.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01969.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01972.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01975.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01978.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01981.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01983.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01984.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01993.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01998.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02004.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02091.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02148.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02261.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02273.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02279.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02287.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02293.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02300.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02302.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02303.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/PEL/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/PEL/splits/00/running_out/PEL_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02490.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02491.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02600.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02601.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02603.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02604.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02654.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02655.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02657.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02658.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02660.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02661.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02684.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02685.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02687.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02688.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02696.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02697.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02733.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02734.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02724.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02725.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02727.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02728.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02783.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02784.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02786.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02787.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02789.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03234.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03235.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03488.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03490.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03491.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03619.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03634.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03667.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03668.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03015.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03016.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03702.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03703.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03708.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03709.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03237.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03238.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02493.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02494.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02648.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02649.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02651.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02652.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02681.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02682.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02690.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02691.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02699.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02700.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02736.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02737.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02774.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02792.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02793.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03228.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03229.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03624.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03625.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03640.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03649.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03652.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03653.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03705.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03706.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03762.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01593.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02597.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03021.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03636.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03765.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03767.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01583.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01586.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01589.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02694.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02731.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02780.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03018.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03022.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03629.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03631.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03660.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03663.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02492.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02495.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02602.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02605.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02650.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02653.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02656.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02659.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02662.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02683.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02686.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02689.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02692.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02698.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02701.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02726.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02729.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02735.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02738.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02776.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02785.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02788.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02791.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02794.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03017.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03230.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03236.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03487.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03489.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03492.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03618.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03620.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03626.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03633.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03635.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03639.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03641.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03650.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03651.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03654.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03669.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03699.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03700.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03701.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03704.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03707.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03710.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03761.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03763.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/PJL/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/PJL/splits/00/running_out/PJL_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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_698_related/HG01099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01103.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01109.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01169.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01172.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01175.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01178.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01184.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01189.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01192.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01199.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01206.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01243.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01249.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/PUR/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/PUR/splits/00/running_out/PUR_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03644.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03643.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03679.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03642.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03673.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03684.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03885.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03886.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03692.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03693.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03740.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03741.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03884.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03743.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03757.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03746.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03888.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03750.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03754.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03756.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03844.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03838.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03849.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03950.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03858.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03887.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03986.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03896.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03898.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03900.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03943.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03755.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03850.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03894.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03897.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03944.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03646.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03645.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03999.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03672.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03680.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03681.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03685.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03686.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03687.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03689.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03690.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03691.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03694.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03695.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03696.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03697.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03698.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03711.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03733.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03736.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03738.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03744.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03745.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03752.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03753.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03760.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03836.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03837.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03846.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03848.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03856.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03895.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03890.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04033.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03947.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03953.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03949.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04035.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04029.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04042.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03995.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03899.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03951.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03857.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03854.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04210.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04075.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04229.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04227.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03945.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03955.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03990.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03991.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03985.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03989.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03998.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04003.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04038.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04039.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04047.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03682.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03683.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03688.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03992.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04036.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04115.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04199.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04204.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04215.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04228.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/STU/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/STU/splits/00/running_out/STU_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20502.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20503.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20504.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20505.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20506.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20507.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20508.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20509.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20510.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20511.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20512.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20513.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20514.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20515.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20516.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20517.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20518.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20519.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20520.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20521.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20522.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20524.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20525.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20527.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20528.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20529.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20530.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20531.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20532.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20533.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20534.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20535.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20536.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20538.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20539.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20540.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20541.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20542.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20543.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20544.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20581.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20582.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20585.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20586.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20587.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20588.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20589.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20752.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20753.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20754.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20755.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20756.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20757.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20758.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20759.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20760.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20761.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20762.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20763.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20764.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20765.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20766.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20767.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20768.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20769.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20770.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20771.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20772.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20773.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20774.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20783.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20785.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20786.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20787.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20792.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20795.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20796.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20797.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20798.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20799.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20800.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20801.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20802.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20803.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20804.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20805.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20806.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20807.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20808.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20809.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20810.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20811.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20812.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20813.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20814.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20815.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20818.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20819.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20821.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20822.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20826.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20827.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20828.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20832.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/TSI/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/TSI/splits/00/running_out/TSI_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18486.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18489.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18498.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18499.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18501.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18502.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18504.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18505.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18507.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18508.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18510.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18511.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18516.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18517.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18519.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18520.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18522.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18523.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18853.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18856.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18858.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18870.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18871.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18907.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18909.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18912.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18916.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19093.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19098.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19102.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19108.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19114.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19116.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19119.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19129.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19131.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19137.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19138.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19143.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19147.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19152.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19153.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19159.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19160.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19171.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19172.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19190.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19200.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19201.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19204.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19206.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19207.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19209.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19210.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19225.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19238.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19257.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18488.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18868.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18873.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18908.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18910.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18923.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18924.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18933.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18934.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19092.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19095.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19096.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19113.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19117.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19118.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19121.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19130.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19149.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19175.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19184.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19185.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19189.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19197.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19198.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19213.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19214.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19223.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19235.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19236.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19247.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19248.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19256.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18865.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18876.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18877.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18878.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18879.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18915.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19222.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18484.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18485.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18487.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18497.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18500.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18503.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18506.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18515.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18518.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18521.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18852.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18854.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18855.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18857.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18859.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18860.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18862.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18869.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18875.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18906.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18911.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18913.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18914.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18925.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18930.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18935.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19094.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19097.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19101.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19103.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19109.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19115.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19120.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19123.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19132.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19139.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19140.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19145.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19148.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19150.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19151.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19154.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19161.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19173.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19174.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19176.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19177.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19186.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19191.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19199.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19202.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19203.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19205.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19208.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19211.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19215.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19221.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19224.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19226.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19237.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19240.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19249.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19258.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/YRI/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/YRI/splits/00/running_out/YRI_00.vcf.gz --max-reads 2000000
+##command=/projects/ps-gymreklab/helia/ensembl/venv_3.9/bin/mergeSTR --vcfs /projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/ACB_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/ASW_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/BEB_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CDX_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CEU_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CHB_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CHS_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CLM_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/ESN_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/FIN_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/GBR_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/GIH_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/GWD_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/IBS_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/ITU_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/JPT_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/KHV_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/LWK_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/MSL_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/MXL_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/PEL_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/PJL_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/PUR_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/STU_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/TSI_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/YRI_filtered.vcf.gz --out /projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/all_pop_filtered_hipstr --vcftype hipstr
+##INFO=<ID=END,Number=1,Type=Integer,Description="Inclusive end coordinate for the repetitive portion of the reference allele">
+##filedate=20220809
+##source="beagle.22Jul22.46e.jar"
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies">
+##INFO=<ID=DR2,Number=A,Type=Float,Description="Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose">
+##INFO=<ID=IMP,Number=0,Type=Flag,Description="Imputed marker">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DS,Number=A,Type=Float,Description="estimated ALT dose [P(RA) + 2*P(AA)]">
+##FORMAT=<ID=AP1,Number=A,Type=Float,Description="estimated ALT dose on first haplotype">
+##FORMAT=<ID=AP2,Number=A,Type=Float,Description="estimated ALT dose on second haplotype">
+##INFO=<ID=START,Number=1,Type=Integer,Description="Inclusive start coodinate for the repetitive portion of the reference allele">
+##INFO=<ID=PERIOD,Number=1,Type=Integer,Description="Length of STR motif">
+##bcftools_annotateVersion=1.15.1+htslib-1.15.1
+##bcftools_annotateCommand=annotate -a hipstr_100.vcf.gz -c INFO/START,INFO/END,INFO/PERIOD -o hipstr_imputed_reheadered_reannotated.vcf.gz -O z hipstr_imputed_reheadered.vcf.gz; Date=Tue Aug  9 08:47:15 2022
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##bcftools_viewVersion=1.19+htslib-1.20
+##bcftools_viewCommand=view -s HG02256,HG02257 -Oz -o hipstr_imputed_merge1.vcf.gz hipstr_imputed.vcf.gz; Date=Tue Jul 23 18:29:28 2024
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG02256	HG02257
+chr1	1007589	Human_STR_297	AAAAAGAAAAAGAAAAGAAAAAAGAAAAAG	AAAAAGAAAAAGAAAAGAAAAAAGAGAAAG	.	PASS	DR2=0;AF=0;END=1007618;START=1007589;PERIOD=6;AC=0;AN=4	GT:DS:AP1:AP2	0|0:0:0:0	0|0:0:0:1
+chr1	1111533	Human_STR_383	CAACAACAACAACAA	CAACAACAA,CAACAACAACAA,CAACAACAACAACAACAA,CGACAACAACAACAA	.	PASS	DR2=0,0,0,0;AF=0,0,0,0;END=1111547;START=1111533;PERIOD=3;AC=0,0,0,0;AN=4	GT:DS:AP1:AP2	0|0:0,0,0,0:0,0,0,0:0,0,0,0	0|0:0,0,0,0:0,0,0,1:0,0,0,1
diff --git a/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge2.vcf b/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge2.vcf
new file mode 100644
index 00000000..010e1267
--- /dev/null
+++ b/trtools/testsupport/sample_vcfs/beagle/hipstr_imputed_merge2.vcf
@@ -0,0 +1,3416 @@
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/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01882.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01883.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01885.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01956.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02014.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01886.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01890.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01889.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02009.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02010.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01914.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01915.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01986.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01958.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01990.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02012.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02053.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02054.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02255.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02256.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02314.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02315.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02281.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02282.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02317.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02318.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01912.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01894.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01879.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01880.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02013.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01896.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01985.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01988.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01989.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02051.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02052.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02095.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02332.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02108.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02111.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02143.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02307.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02308.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02283.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02309.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02284.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02322.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02323.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02325.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02337.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02330.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02339.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02343.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02419.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02420.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02427.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02429.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02433.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02442.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02445.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02489.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02449.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02450.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02470.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02471.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02479.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02484.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02485.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02511.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02496.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02497.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02508.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02537.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02439.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02455.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02476.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02477.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02481.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02501.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02502.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02505.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02536.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02541.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02545.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02546.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02549.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02554.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02555.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02557.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02558.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02577.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02580.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01884.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01887.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01888.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01891.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01895.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01897.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01916.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01959.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01960.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01987.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02011.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02055.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02145.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02257.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02258.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02280.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02316.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02321.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02451.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ACB/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ACB/splits/00/running_out/ACB_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19625.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19700.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19701.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19703.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19704.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19707.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19711.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19712.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19713.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19818.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19819.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19834.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19835.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19900.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19901.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19904.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19908.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19909.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19914.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19916.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19920.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19921.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19982.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20126.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20276.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20278.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20281.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20282.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20287.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20289.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20291.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20294.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20296.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20299.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20314.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20317.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20332.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20340.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20342.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20346.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20348.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20356.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20357.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20359.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19922.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19923.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19984.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20298.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20339.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20351.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20412.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19913.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20274.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20318.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20320.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20321.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20355.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20362.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19702.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19705.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19828.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19836.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19902.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19918.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19919.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19924.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19983.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA20128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA20129.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA20279.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA20358.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ASW/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ASW/splits/00/running_out/ASW_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03007.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03615.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03616.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03793.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03796.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03800.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03803.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03802.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03815.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03814.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03824.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03823.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03826.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03830.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03829.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03833.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03832.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03914.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03913.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03941.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03940.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04155.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04156.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03607.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03805.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03908.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03907.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03926.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03925.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03594.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03595.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03809.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03808.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03009.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03812.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03817.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03902.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03012.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03905.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03911.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03910.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03916.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03919.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03928.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03931.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03585.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03937.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03934.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03589.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04159.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03593.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04186.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03598.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04158.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04185.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04131.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04134.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04140.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04173.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04182.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04183.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03821.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03922.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04180.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03600.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03603.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03604.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03611.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03920.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04152.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04153.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04161.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04162.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04164.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04171.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04176.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04177.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04188.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04189.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04194.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04195.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03008.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03596.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03605.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03606.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03617.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03794.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03795.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03797.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03798.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03799.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03801.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03804.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03806.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03807.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03816.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03825.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03831.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03834.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03904.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03906.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03909.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03915.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03927.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03929.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03930.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03942.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04132.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04133.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04135.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04136.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04147.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04148.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04149.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04150.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04151.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04157.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04160.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04174.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04175.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04184.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04187.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04191.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04192.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04193.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/BEB/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/BEB/splits/00/running_out/BEB_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00759.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00766.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00844.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00879.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00956.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00978.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00982.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01028.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01029.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01031.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01046.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01794.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01795.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01796.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01797.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01798.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01799.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01800.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01801.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01802.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01804.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01805.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01806.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01807.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01808.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01809.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01810.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01811.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01812.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01813.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02151.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01815.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01816.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01817.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02152.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02153.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02154.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02155.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02156.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02164.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02165.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02166.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02178.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02179.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02180.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02181.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02182.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02184.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02185.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02186.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02187.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02188.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02190.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02373.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02394.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02396.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02397.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02250.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02351.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02353.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02355.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02356.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02360.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02364.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02367.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02371.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02374.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02375.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02379.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02380.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02382.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02383.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02384.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02385.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02386.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02389.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02390.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02391.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02392.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02395.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02398.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02399.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02401.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02402.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02406.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02407.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02409.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02408.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02410.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CDX/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CDX/splits/00/running_out/CDX_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06985.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06986.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06994.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07000.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07037.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07051.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07347.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07357.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA10847.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA10851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11829.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11830.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11831.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11832.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11840.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11894.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11918.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11919.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11920.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11931.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11992.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11994.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11995.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12003.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12004.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12005.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12043.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12044.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12045.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12154.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12155.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12156.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12234.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12249.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12287.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12414.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12489.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12716.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12717.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12749.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12750.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12751.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12760.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12761.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12762.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12763.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12776.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12812.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12813.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12814.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12815.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12828.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12873.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12878.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06984.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA06989.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11843.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11892.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11893.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11930.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12058.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12272.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12273.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12275.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12282.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12283.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12286.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12340.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12341.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12342.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12347.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12348.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12383.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12399.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12400.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12413.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12718.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12748.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12777.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12827.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12829.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12842.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12843.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12889.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12890.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA07048.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11932.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA11933.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12046.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12830.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA12546.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA06991.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA06993.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA06995.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA06997.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07014.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07022.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07029.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07031.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07034.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07045.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07055.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07345.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07346.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07348.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07349.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA07435.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10830.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10831.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10835.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10836.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10837.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10838.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10839.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10840.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10842.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10843.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10845.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10846.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10852.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10854.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10855.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10856.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10857.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10859.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10860.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA10865.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11839.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11882.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11891.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA11993.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12057.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12145.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12236.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12248.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12264.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12274.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12329.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12335.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12336.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12343.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12344.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12376.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12386.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12485.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12707.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12739.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12740.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12752.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12753.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12766.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12767.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12801.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12802.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12817.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12818.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12832.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12865.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12875.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12877.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12891.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA12892.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/CEU/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/CEU/splits/00/running_out/CEU_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18526.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18532.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18537.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18542.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18545.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18547.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18550.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18552.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18555.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18558.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18561.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18562.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18563.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18564.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18566.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18570.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18571.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18572.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18573.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18577.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18579.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18582.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18592.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18593.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18603.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18605.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18608.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18609.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18638.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18614.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18530.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18534.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18536.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18543.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18544.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18546.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18548.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18549.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18557.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18559.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18595.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18596.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18597.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18599.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18602.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18606.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18610.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18611.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18612.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18613.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18615.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18616.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18617.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18618.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18619.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18620.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18621.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18622.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18623.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18624.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18625.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18626.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18627.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18628.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18630.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18631.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18632.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18633.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18634.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18635.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18636.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18637.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18639.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18640.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18641.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18642.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18643.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18645.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18647.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18740.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18745.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18747.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18748.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18749.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18757.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18525.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18528.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18531.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18533.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18535.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18538.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18539.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18541.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18553.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18560.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18565.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18567.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18574.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18591.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18629.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18644.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18646.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18648.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CHB/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CHB/splits/00/running_out/CHB_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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--fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CHS/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/CHS/splits/00/running_out/CHS_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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/HG01391.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01433.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01439.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01457.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01463.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01466.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01490.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01493.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01496.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01499.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01552.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/CLM/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/CLM/splits/00/running_out/CLM_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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--fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ESN/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/ESN/splits/00/running_out/ESN_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00171.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00173.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00174.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00176.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00177.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00178.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00179.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00180.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00181.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00182.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00183.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00185.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00186.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00187.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00188.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00189.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00190.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00266.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00267.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00268.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00269.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00271.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00272.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00273.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00306.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00308.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00309.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00311.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00313.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00315.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00318.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00319.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00320.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00321.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00323.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00327.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00328.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00335.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00336.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00337.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00338.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00339.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00342.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00343.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00344.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00345.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00346.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00349.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00350.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00351.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00353.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00355.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00356.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00357.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00358.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00360.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00361.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00362.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00364.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00365.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00366.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00367.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00368.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00369.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00371.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00372.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00373.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00375.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00376.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00378.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00379.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00380.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00381.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00382.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00384.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00274.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00275.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00276.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00277.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00278.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00280.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00281.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00282.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00284.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00285.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00310.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00324.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00325.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00326.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00329.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00330.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00331.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00332.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00341.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00383.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00288.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00290.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00304.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/FIN/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/FIN/splits/00/running_out/FIN_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00096.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00097.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00101.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00102.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00103.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00105.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00108.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00109.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00110.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00111.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00112.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00113.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00114.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00115.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00116.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00117.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00120.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00129.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00130.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00131.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00132.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00133.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00136.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00137.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00138.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00139.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00140.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00143.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00145.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00148.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00149.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00150.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00151.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00155.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00157.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00158.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00160.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00233.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00234.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00235.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00238.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00240.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00255.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00118.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00119.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00121.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00123.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00125.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00126.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00159.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00231.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00232.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00236.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00237.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00242.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00243.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00244.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00245.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00252.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00253.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00254.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00256.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00257.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00258.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00259.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00260.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00261.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00262.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00263.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00264.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00265.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00154.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00246.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00250.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG00251.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01789.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01791.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02215.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/GBR/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/GBR/splits/00/running_out/GBR_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20845.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20846.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20847.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20849.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20850.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20852.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20853.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20854.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20856.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20858.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20859.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20862.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20866.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20869.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20870.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20875.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20876.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20877.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20878.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20882.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20884.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20885.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20886.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20887.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20888.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20889.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20890.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20891.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20892.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20894.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20895.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20896.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20897.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20899.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20900.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20901.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20902.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20903.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20904.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20906.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20908.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20910.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20911.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21086.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21088.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21089.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21090.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21091.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21092.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21094.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21097.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21098.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21101.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21102.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21103.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21104.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21105.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21108.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21109.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21110.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21111.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21112.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21113.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21115.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21116.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21117.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21118.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21119.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21120.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21123.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21125.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21130.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21133.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21135.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21137.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21143.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20868.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20905.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21087.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21093.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21095.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21114.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21124.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21126.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA21129.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/GIH/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/GIH/splits/00/running_out/GIH_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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1000Genomes/additional_698_related/HG03540.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/GWD/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/GWD/splits/00/running_out/GWD_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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--fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/IBS/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/IBS/splits/00/running_out/IBS_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03713.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03716.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03714.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03717.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03722.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03730.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03727.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03729.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03731.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03771.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03770.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03882.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03781.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03773.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03772.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03786.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03784.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03787.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03788.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03789.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03869.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03862.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03978.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03971.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03974.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03976.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03973.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04002.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04017.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04026.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03977.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03780.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03718.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04018.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03742.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03779.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03777.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03785.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03792.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03782.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03873.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03870.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03963.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03960.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03968.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03720.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04025.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04020.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04014.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04015.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04022.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04063.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04093.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04118.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03774.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04001.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03866.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03969.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04023.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04060.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04090.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04054.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04061.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04062.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04059.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04076.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04080.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04094.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04096.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04098.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04209.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04198.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04200.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04206.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04202.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04211.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04212.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04222.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04214.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04216.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04219.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04225.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04235.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04238.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03875.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03965.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04070.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03868.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03871.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03967.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03719.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03721.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03725.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03732.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04217.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/ITU/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/ITU/splits/00/running_out/ITU_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18940.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18942.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18943.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18944.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18945.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18947.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18948.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18949.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18951.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18952.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18953.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18956.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18959.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18960.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18961.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18964.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18965.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18967.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18968.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18969.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18970.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18971.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18972.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18973.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18974.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18975.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18976.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18980.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18981.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19005.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18939.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18941.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18946.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18954.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18957.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18962.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18963.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18966.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18977.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18978.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18979.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18987.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18990.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18991.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18992.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18993.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18994.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18995.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18997.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18998.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18999.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19000.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19001.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19002.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19003.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19007.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19009.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19010.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19012.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19054.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19055.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19057.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19058.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19059.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19060.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19062.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19063.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19064.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19065.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19066.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19067.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19068.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19070.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19072.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19074.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19075.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19076.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19077.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19078.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19079.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19080.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19081.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19082.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19083.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19084.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19085.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19086.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19087.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19088.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18950.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18982.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18983.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18984.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18985.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18986.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18988.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18989.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19004.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19011.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19089.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19090.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19091.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/JPT/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/JPT/splits/00/running_out/JPT_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02017.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02016.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02020.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02023.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02026.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02025.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02029.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02028.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02058.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02057.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02070.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02069.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02073.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02072.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02076.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02075.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02079.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02078.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02082.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02081.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02085.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02084.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02134.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02133.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01841.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01595.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01596.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01597.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01598.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01599.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01600.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01840.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01842.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01843.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01844.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01845.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01846.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01847.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01848.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01849.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01850.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01852.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01853.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01855.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01857.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01858.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01859.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01860.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01862.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01865.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01866.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01868.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01869.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01870.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01871.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01873.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01878.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02048.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02049.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02086.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02087.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02088.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02138.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02139.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02140.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02113.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02121.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02032.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02031.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02050.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02035.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02040.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02047.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02061.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02060.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02064.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02067.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02116.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02131.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02130.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02137.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02136.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02512.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02513.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02521.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02522.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02015.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02018.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02024.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02027.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02030.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02059.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02068.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02071.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02074.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02077.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02080.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02083.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02120.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02126.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02129.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02132.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02135.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02514.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02523.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02524.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02525.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02526.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/KHV/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EAS/KHV/splits/00/running_out/KHV_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19017.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19020.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19023.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19024.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19025.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19026.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19027.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19028.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19030.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19031.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19035.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19036.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19037.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19038.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19041.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19042.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19043.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19307.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19308.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19309.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19310.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19312.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19314.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19315.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19316.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19317.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19318.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19319.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19320.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19321.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19323.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19324.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19327.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19328.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19331.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19332.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19334.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19338.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19346.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19347.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19350.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19351.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19355.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19360.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19372.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19374.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19375.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19376.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19377.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19378.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19379.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19380.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19383.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19384.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19385.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19390.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19391.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19393.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19394.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19395.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19397.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19399.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19401.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19403.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19404.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19428.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19429.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19430.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19431.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19434.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19435.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19436.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19437.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19438.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19439.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19440.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19443.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19445.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19446.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19448.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19449.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19451.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19452.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19454.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19455.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19456.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19457.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19461.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19462.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19463.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19466.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19467.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19468.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19471.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19472.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19473.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19474.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19475.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/LWK/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/LWK/splits/00/running_out/LWK_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03052.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03057.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03058.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03078.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03084.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03085.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03096.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03097.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03397.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03451.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03452.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03464.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03469.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03472.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03470.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03473.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03081.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03088.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03209.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03212.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03055.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03376.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03380.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03385.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03388.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03401.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03419.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03061.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03428.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03433.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03439.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03442.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03445.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03446.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03460.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03461.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03478.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03479.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03066.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03069.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03072.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03410.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03436.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03437.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03449.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03458.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03476.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03484.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03485.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03547.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03548.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03556.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03557.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03391.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03455.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03559.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03563.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03565.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03571.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03572.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03575.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03577.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03578.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03583.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03054.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03060.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03063.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03064.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03073.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03074.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03077.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03079.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03082.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03086.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03091.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03095.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03224.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03225.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03378.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03382.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03394.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03432.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03457.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03558.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03567.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03056.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03065.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03098.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03438.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03453.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03454.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03456.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03480.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03486.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03574.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03576.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03579.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03582.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03584.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/MSL/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/MSL/splits/00/running_out/MSL_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19648.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19649.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19651.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19652.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19654.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19655.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19657.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19658.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19661.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19663.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19664.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19669.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19670.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19676.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19678.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19679.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19681.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19682.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19684.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19716.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19717.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19719.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19720.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19722.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19723.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19725.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19726.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19728.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19729.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19731.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19732.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19746.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19747.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19749.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19750.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19755.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19756.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19758.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19759.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19761.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19762.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19770.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19771.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19773.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19774.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19776.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19777.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19779.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19780.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19782.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19783.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19785.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19786.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19788.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19789.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19794.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19795.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19734.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19735.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19740.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19741.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19752.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19764.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19792.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19650.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19653.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19656.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19659.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19660.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19662.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19665.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19671.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19675.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19677.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19680.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19683.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19685.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19686.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19718.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19721.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19724.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19727.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19730.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19733.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19748.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19751.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19757.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19760.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19763.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19772.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19781.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19784.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19787.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19796.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/MXL/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/MXL/splits/00/running_out/MXL_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01565.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01566.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01571.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01572.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01577.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01578.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01918.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01892.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01893.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01920.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01921.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01923.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01924.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01926.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01927.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01932.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01933.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01935.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01936.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01938.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01939.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01941.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01942.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01944.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01945.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01947.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01948.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01950.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01951.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01953.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01954.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01967.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01968.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01970.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01971.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01974.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01973.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01977.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01976.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01979.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01980.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01991.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01992.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02008.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01997.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02002.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02003.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02090.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02089.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02104.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02105.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02285.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02286.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02301.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01982.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02147.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02259.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02260.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02271.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02272.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02277.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02278.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02291.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02292.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02299.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02298.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01961.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01965.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02102.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02150.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02252.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02253.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02262.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02265.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02266.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02274.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02275.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02304.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02312.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02345.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02348.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02425.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01567.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01573.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01579.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01898.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01919.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01922.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01925.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01928.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01934.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01937.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01940.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01943.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01946.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01949.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01952.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01955.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01969.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01972.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01975.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01978.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01981.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01983.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01984.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01993.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01998.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02004.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02091.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02148.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02261.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02273.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02279.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02287.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02293.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02300.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02302.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02303.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/PEL/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/PEL/splits/00/running_out/PEL_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02490.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02491.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02600.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02601.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02603.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02604.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02654.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02655.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02657.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02658.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02660.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02661.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02684.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02685.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02687.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02688.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02696.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02697.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02733.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02734.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02724.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02725.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02727.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02728.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02783.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02784.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02786.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02787.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02789.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03234.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03235.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03488.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03490.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03491.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03619.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03634.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03667.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03668.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03015.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03016.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03702.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03703.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03708.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03709.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03237.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03238.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02493.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02494.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02648.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02649.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02651.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02652.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02681.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02682.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02690.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02691.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02699.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02700.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02736.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02737.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02774.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02792.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02793.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03228.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03229.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03624.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03625.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03640.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03649.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03652.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03653.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03705.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03706.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03762.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01593.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02597.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03021.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03636.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03765.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03767.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01583.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01586.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG01589.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02694.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02731.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG02780.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03018.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03019.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03022.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03629.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03631.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03660.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03663.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02492.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02495.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02602.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02605.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02650.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02653.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02656.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02659.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02662.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02683.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02686.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02689.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02692.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02698.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02701.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02726.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02729.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02735.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02738.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02776.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02785.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02788.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02791.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG02794.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03017.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03230.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03236.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03487.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03489.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03492.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03618.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03620.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03626.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03633.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03635.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03639.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03641.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03650.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03651.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03654.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03669.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03699.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03700.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03701.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03704.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03707.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03710.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03761.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03763.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/PJL/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/PJL/splits/00/running_out/PJL_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams 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_698_related/HG01099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01103.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01109.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01169.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01172.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01175.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01178.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01184.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01189.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01192.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01199.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01206.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01243.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG01249.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/PUR/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AMR/PUR/splits/00/running_out/PUR_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03644.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03643.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03679.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03642.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03673.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03684.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03885.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03886.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03692.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03693.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03740.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03741.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03884.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03743.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03757.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03746.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03888.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03750.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03754.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03756.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03844.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04006.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03838.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03849.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03950.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03858.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03887.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03986.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03896.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03898.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03900.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03943.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03755.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03850.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03894.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03897.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03944.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03646.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03645.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03999.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03672.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03680.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03681.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03685.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03686.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03687.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03689.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03690.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03691.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03694.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03695.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03696.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03697.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03698.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03711.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03733.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03736.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03738.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03744.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03745.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03752.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03753.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03760.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03836.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03837.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03846.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03848.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03851.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03856.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03895.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03890.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04033.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03947.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03953.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03949.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04035.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04029.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04042.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03995.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03899.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03951.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03857.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03854.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04210.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04075.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04229.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04227.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03945.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03955.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03990.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03991.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03985.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03989.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG03998.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04003.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04038.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04039.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04047.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/HG04106.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03682.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03683.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03688.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG03992.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04036.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04115.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04199.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04204.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04215.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/HG04228.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/STU/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//SAS/STU/splits/00/running_out/STU_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20502.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20503.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20504.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20505.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20506.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20507.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20508.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20509.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20510.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20511.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20512.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20513.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20514.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20515.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20516.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20517.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20518.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20519.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20520.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20521.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20522.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20524.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20525.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20527.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20528.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20529.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20530.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20531.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20532.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20533.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20534.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20535.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20536.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20538.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20539.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20540.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20541.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20542.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20543.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20544.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20581.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20582.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20585.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20586.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20587.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20588.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20589.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20752.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20753.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20754.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20755.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20756.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20757.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20758.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20759.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20760.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20761.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20762.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20763.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20764.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20765.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20766.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20767.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20768.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20769.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20770.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20771.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20772.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20773.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20774.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20775.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20778.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20783.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20785.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20786.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20787.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20790.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20792.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20795.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20796.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20797.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20798.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20799.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20800.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20801.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20802.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20803.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20804.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20805.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20806.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20807.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20808.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20809.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20810.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20811.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20812.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20813.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20814.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20815.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20818.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20819.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20821.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20822.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20826.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20827.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20828.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA20832.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/TSI/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//EUR/TSI/splits/00/running_out/TSI_00.vcf.gz --max-reads 2000000
+##command=HipSTR-v0.6.2 --bams /projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18486.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18489.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18498.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18499.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18501.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18502.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18504.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18505.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18507.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18508.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18510.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18511.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18516.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18517.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18519.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18520.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18522.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18523.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18853.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18856.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18858.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18861.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18870.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18871.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18907.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18909.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18912.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18916.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19093.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19098.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19099.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19102.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19108.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19114.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19116.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19119.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19129.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19131.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19137.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19138.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19141.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19143.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19144.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19147.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19152.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19153.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19159.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19160.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19171.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19172.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19190.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19200.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19201.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19204.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19206.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19207.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19209.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19210.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19225.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19238.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19239.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19257.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18488.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18867.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18868.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18873.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18908.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18910.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18917.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18923.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18924.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18933.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18934.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19092.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19095.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19096.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19107.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19113.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19117.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19118.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19121.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19130.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19146.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19149.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19175.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19184.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19185.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19189.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19197.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19198.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19213.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19214.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19223.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19235.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19236.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19247.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19248.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19256.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18864.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18865.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18876.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18877.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18878.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18879.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18881.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18915.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA19222.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/cram/NA18874.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18484.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18485.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18487.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18497.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18500.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18503.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18506.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18515.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18518.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18521.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18852.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18854.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18855.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18857.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18859.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18860.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18862.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18863.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18869.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18872.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18875.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18906.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18911.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18913.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18914.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18925.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18930.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA18935.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19094.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19097.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19100.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19101.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19103.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19109.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19115.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19120.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19122.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19123.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19127.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19128.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19132.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19139.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19140.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19142.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19145.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19148.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19150.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19151.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19154.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19161.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19173.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19174.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19176.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19177.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19186.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19191.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19199.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19202.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19203.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19205.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19208.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19211.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19215.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19221.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19224.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19226.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19237.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19240.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19249.final.cram,/projects/ps-gymreklab/resources/datasets/1000Genomes/additional_698_related/NA19258.final.cram --fasta /projects/ps-gymreklab/resources/dbase/human/hg38_full_plus_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa --regions /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/YRI/splits/regions/00.txt --str-vcf /projects/ps-gymreklab/mousavi/results/1000genomes/hipstr_outs//AFR/YRI/splits/00/running_out/YRI_00.vcf.gz --max-reads 2000000
+##command=/projects/ps-gymreklab/helia/ensembl/venv_3.9/bin/mergeSTR --vcfs /projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/ACB_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/ASW_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/BEB_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CDX_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CEU_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CHB_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CHS_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/CLM_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/ESN_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/FIN_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/GBR_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/GIH_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/GWD_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/IBS_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/ITU_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/JPT_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/KHV_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/LWK_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/MSL_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/MXL_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/PEL_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/PJL_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/PUR_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/STU_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/TSI_filtered.vcf.gz,/projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/filtered/YRI_filtered.vcf.gz --out /projects/ps-gymreklab/helia/ensembl/1000G_calls/hipstr/all_pop_filtered_hipstr --vcftype hipstr
+##INFO=<ID=END,Number=1,Type=Integer,Description="Inclusive end coordinate for the repetitive portion of the reference allele">
+##filedate=20220809
+##source="beagle.22Jul22.46e.jar"
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies">
+##INFO=<ID=DR2,Number=A,Type=Float,Description="Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose">
+##INFO=<ID=IMP,Number=0,Type=Flag,Description="Imputed marker">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DS,Number=A,Type=Float,Description="estimated ALT dose [P(RA) + 2*P(AA)]">
+##FORMAT=<ID=AP1,Number=A,Type=Float,Description="estimated ALT dose on first haplotype">
+##FORMAT=<ID=AP2,Number=A,Type=Float,Description="estimated ALT dose on second haplotype">
+##INFO=<ID=START,Number=1,Type=Integer,Description="Inclusive start coodinate for the repetitive portion of the reference allele">
+##INFO=<ID=PERIOD,Number=1,Type=Integer,Description="Length of STR motif">
+##bcftools_annotateVersion=1.15.1+htslib-1.15.1
+##bcftools_annotateCommand=annotate -a hipstr_100.vcf.gz -c INFO/START,INFO/END,INFO/PERIOD -o hipstr_imputed_reheadered_reannotated.vcf.gz -O z hipstr_imputed_reheadered.vcf.gz; Date=Tue Aug  9 08:47:15 2022
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##bcftools_viewVersion=1.19+htslib-1.20
+##bcftools_viewCommand=view -s HG02258,HG02280 -Oz -o hipstr_imputed_merge2.vcf.gz hipstr_imputed.vcf.gz; Date=Tue Jul 23 18:30:08 2024
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG02258	HG02280
+chr1	1007589	Human_STR_297	AAAAAGAAAAAGAAAAGAAAAAAGAAAAAG	AAAAAGAAAAAGAAAAGAAAAAAGAGAAAG	.	PASS	DR2=0;AF=0;END=1007618;START=1007589;PERIOD=6;AC=0;AN=4	GT:DS:AP1:AP2	0|0:0:0:0.5	0|0:0:0:0.25
+chr1	1111533	Human_STR_383	CAACAACAACAACAA	CAACAACAA,CAACAACAACAA,CAACAACAACAACAACAA,CGACAACAACAACAA	.	PASS	DR2=0,0,0,0;AF=0,0,0,0;END=1111547;START=1111533;PERIOD=3;AC=0,0,0,0;AN=4	GT:DS:AP1:AP2	0|0:0,0,0,0:0,0,0,0:0,0,0,0.25	0|0:0,0,0,0:0,0,0,0:0,0,0,0.5
diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..48bbe8cfc1701cdb906bf88e569d322f78dd88e7
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diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz.tbi b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge1.vcf.gz.tbi
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diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz
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diff --git a/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz.tbi b/trtools/testsupport/sample_vcfs/mergeSTR_vcfs/hipstr_imputed_merge2.vcf.gz.tbi
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