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, additional output includes both a VCF and an MAF file with the set of SNVs shared by two or more callers, and a Venn Diagram showing counts of shared and private SNVs.

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 is an older tool yielding high specificity single nucleotide somatic variants.

  • Strelka2 uses candidate indels from Manta and calls somatic short mutations (single nucleotide and small indel), filtered with a random forest model.

  • GATK Mutect2 calls somatic short mutations via local assembly of haplotypes.

  • MuSE accounts for tumor heterogeneity and calls single nucleotide somatic variants.