Somatic SV Workflow

With modifications for CWL integration

Contact Matt Wyczalkowski ([email protected]) with questions

Versions

Versions are those indicated in DCC Analysis Summary for CPTAC3 project

Version 2.0

• Associated with image mwyczalkowski/somatic_sv:20220217
• Manta 1.6.0
• Support for tumor/normal and tumor-only modes
• Files returned, currently unfiltered:
  • Tumor-normal
    • candidateSmallIndels.vcf.gz
    • candidateSV.vcf.gz
    • diploidSV.vcf.gz
    • somaticSV.vcf.gz
  • Tumor-only
    • candidateSmallIndels.vcf.gz
    • candidateSV.vcf.gz
    • tumorSV.vcf.gz

Version 1.2

• Associated with CWL file "SomaticSV.cwl"
  • this is the version used for CPTAC3 processing
• Docker image: mwyczalkowski/somatic_sv:20200518
• Manta 1.6.0
• Filters: Only select the variants from somaticSV.vcf.gz output which pass the following criteria:
  • Sample site depth is less than 3x the median chromosome depth near one or both variant breakends
  • Somatic score is greater than 30
  • For a small variant (<1000 bases) in the normal sample, the fraction of reads with MAPQ0 around either breakend doesn't exceed 0.4
• BAM files evidence_0 and evidence_1 generated with Manta argument --generateEvidenceBam

Version 1.1

• Manta 1.4.0 with tumor and normal sequence data
• Filtering as in v1.2, no BAM evidence files returned

Run Notes

In general, SomaticSV is run using CromwellRunner

Install SomaticSV

git clone --recurse-submodules https://github.com/ding-lab/SomaticSV.git

Development notes

Demo data

For development and testing purposes, we distribute Demo data obtained from Manta distribution in demo/demo_data directory, consisting of small tumor/normal BAM files and a reference. Prior to testing, need to uncompress the reference with,

tar -xvjf Homo_sapiens_assembly19.COST16011_region.fa.tar.bz2

GitHub Contact Matt Wyczalkowski ([email protected]) with questions