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sorelfitzgibbon committed Aug 7, 2023
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- [License](#license)

## Overview
The call-sSNV nextflow pipeline performs somatic SNV calling given a pair of tumor/normal BAM files. Four somatic SNV callers are available: SomaticSniper, Strelka2, Mutect2 and MuSE. The user may request one or more callers, and each caller produces an independently generated filtered VCF file. If two or more callers are requested, a Venn Diagram is produced showing counts of shared and private variants as well as VCF and MAF files with the set of variants shared by two or more tool outputs.
The call-sSNV nextflow pipeline performs somatic SNV calling given a pair of tumor/normal BAM files. Four somatic SNV callers are available: SomaticSniper, Strelka2, Mutect2 and MuSE. The user may request one or more callers, and each caller produces an independently generated filtered VCF file.

SomaticSniper, Strelka2, and MuSE require there to be **exactly one pair of input tumor/normal** BAM files, but Mutect2 will take tumor-only input (no paired normal), as well as tumor/normal BAM pairs from multiple samples from the same individual.
If two or more callers are requested, additional output includes VCF and MAF files with the set of variants shared by two or more callers as well as a Venn Diagram showing counts of shared and private variants.

SomaticSniper, Strelka2, and MuSE require there to be **exactly one pair of input tumor/normal** BAM files, but Mutect2 will take tumor-only input (no paired normal), as well as tumor/normal BAM pairs for multiple samples from the same individual.

### Somatic SNV callers:
* [SomaticSniper](https://github.com/genome/somatic-sniper) is an older tool yielding high specificity single nucleotide somatic variants.

* [Strelka2](https://github.com/Illumina/strelka) here uses candidate indels from `Manta` and calls somatic short mutations (single nucleotide and small indel) filtered with a random forest model.
* [Strelka2](https://github.com/Illumina/strelka) uses candidate indels from `Manta` and calls somatic short mutations (single nucleotide and small indel), filtered with a random forest model.

* [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2) calls somatic short mutations via local assembly of haplotypes.

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