implement delly/insurveyor

snakepit/short_reads.smk

@@ -0,0 +1,90 @@
+rule all:
+    input:
+        'SR_SV/cohort.delly.forced.vcf.gz',
+        expand('SR_SV/{sample}_{caller}',caller=('insurveyor',),sample=config['HiFi'])
+
+rule picard_add_MQ:
+    input:
+        '/cluster/work/pausch/inputs/bam/BTA_eQTL/{sample}.bam'
+    output:
+        multiext('SR_SV/{sample}.bam','','.bai')
+    envmodules:
+        'gcc/11.4.0',
+        'picard/3.1.1'
+    threads: 1
+    resources:
+        mem_mb = 7500
+    shell:
+        '''
+        picard FixMateInformation -I {input} -O {output[0]}
+        samtools index {output[0]}
+        '''
+
+rule insurveyor:
+    input:
+        rules.picard_add_MQ.output
+    output:
+        _dir = directory('SR_SV/{sample}_insurveyor'),
+        #vcf = 'SR_SV/{sample}.insurveyor.vcf.gz'
+    threads: 4
+    resources:
+        mem_mb = 5000
+    shell:
+        '''
+        mkdir -p {output._dir}
+        python /cluster/work/pausch/alex/software/INSurVeyor/insurveyor.py --threads {threads} --samplename {wildcards.sample} {input[0]} {output._dir} {config[reference]}
+        '''
+
+rule delly_call_denovo:
+    input:
+        '/cluster/work/pausch/inputs/bam/BTA_eQTL/{sample}.bam'
+    output:
+        'SR_SV/{sample}.delly.denovo.bcf'
+    threads: 4
+    resources:
+        mem_mb = 4000
+    shell:
+        '''
+        /cluster/work/pausch/alex/software/delly/src/delly call -g {config[reference]} -o {output} {input}
+        bcftools index {output}
+        '''
+
+rule delly_merge:
+    input:
+        expand(rules.delly_call_denovo.output,sample=config['HiFi'])
+    output:
+        'SR_SV/cohort.delly.denovo.bcf'
+    threads: 4
+    resources:
+        mem_mb = 2500
+    shell:
+        '''
+        /cluster/work/pausch/alex/software/delly/src/delly merge --precise --pass --minsize 50 --vaf 0.01 -o {output} {input}
+        '''
+
+rule delly_call_forced:
+    input:
+        bam = '/cluster/work/pausch/inputs/bam/BTA_eQTL/{sample}.bam',
+        panel = rules.delly_merge.output
+    output:
+        'SR_SV/{sample}.delly.forced.vcf.gz'
+    threads: 4
+    resources:
+        mem_mb = 4000
+    shell:
+        '''
+        /cluster/work/pausch/alex/software/delly/src/delly call -g {config[reference]} -v {input.panel} -o $TMPDIR/sample.bcf {input.bam}
+        bcftools view -o {output} $TMPDIR/sample.bcf
+        tabix -fp vcf {output}
+        '''
+
+rule bcftools_merge:
+    input:
+        expand(rules.delly_call_forced.output,sample=config['HiFi'])
+    output:
+        'SR_SV/cohort.delly.forced.vcf.gz'
+    shell:
+        '''
+        bcftools merge -m id -o {output} {input}
+        tabix -fp vcf {output}
+        '''