Exclude normal groups from somatic candidate sets (first step of #168) - #170
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Normal groups are germline references, not neoantigen candidate sources, but get_snvs / get_shortindels / get_longindels combined *all* groups -- so the matched normal's germline calls (e.g. 890K on a TESLA sample) were merged into the "somatic" set. Add a somatic_groups() helper (tumor groups only, per SAMPLES[sample]["normal"]) and use it in the three somatic combines. First step of #168 (germline subtraction). Still TODO there: paired Mutect2 (-normal) for tumor groups with a matched normal, RNA bcftools-isec vs the normal-group germline (wiring up the dead final HaplotypeCaller round), distinct RG SM tags, gnomAD fallback, and the same exclusion for exitron/fusion/altsplicing.
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Summary
Fixed
Tumor-only Mutect2 does no germline subtraction, and
get_snvs/get_shortindels/get_longindelscombined all groups — so a matched normal's calls (essentially germline) were merged into the "somatic" set (~890K SNVs on a TESLA normal). Add asomatic_groups()helper that returns tumor groups only (viaSAMPLES[sample]["normal"]) and use it in the three somatic combines. The normal is a germline reference, not a neoantigen candidate source.First, self-contained step of #168 (paired somatic calling). The rest — paired Mutect2 (
-normal), RNAbcftools isecvs the normal-group germline, RGSM:{sample}_{group}, gnomAD fallback — follows in a dedicated PR.Validation
combine_somatic_SNVs_m2now pulls only tumor groups (normal excluded).get_countsdeliberately unchanged (quantification still covers all groups).QC