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Somatic SV Workflow

With modifications for CWL integration

Contact Matt Wyczalkowski (m.wyczalkowski@wustl.edu) 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 (m.wyczalkowski@wustl.edu) with questions