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somatic-signatures

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Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.

When to use

• Extracting mutational signatures from somatic VCFs
• Characterizing DNA-damage etiology
• Identifying HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU, platinum, and colibactin processes
• Routing PARP inhibitor decisions
• Auditing de novo extraction vs refit choice for cohort size
• Mapping dominant signatures to etiology
• Flagging clinical actionability

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