processing_description.v2.0.txt

# Somatic SV Workflow

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
- Manta 1.6.0
  - note, all results associated with v1.2, which used image mwyczalkowski/somatic_sv:20200518, was in fact Manta 1.6.0 rather
    than 1.4.0 as was previously indicated
- 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

[Manta](https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md)
[GitHub](https://github.com/ding-lab/SomaticSV.git)
Contact Matt Wyczalkowski (m.wyczalkowski@wustl.edu) with questions