domains / families / science / somatic-variant-pipeline

somatic-variant-pipeline

separate

Chains a somatic (tumor-normal) SNV/indel and structural-variant pipeline end to end with GATK Mutect2 (or Strelka2), wiring the somatic-specific machinery - panel-of-normals and gnomAD germline-resource priors, GetPileupSummaries/CalculateContamination, and LearnReadOrientationModel FFPE/oxoG orientation-bias filtering fed into FilterMutectCalls. Use when calling somatic mutations from a tumor-normal pair (or tumor-only with PoN caveats), deciding which artifact filter removes which class of false positive, reasoning about VAF/purity/ploidy and clonal-vs-subclonal detection, adding somatic SV/CNV or TMB/MSI/signatures, or routing variants to AMP/ASCO/CAP tier and oncogenicity interpretation (never germline ACMG).

When to use

• calling somatic mutations from a tumor-normal pair
• tumor-only calling with PoN caveats
• deciding which artifact filter removes which class of false positive
• reasoning about VAF/purity/ploidy and clonal-vs-subclonal detection
• adding somatic SV/CNV or TMB/MSI/signatures
• routing variants to AMP/ASCO/CAP tier and oncogenicity interpretation

When not to use

• germline ACMG interpretation

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