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feat(pon): scatter PoN Mutect2; fix(freebayes): 1.3.10 - #31
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…30) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
… output with vcflib 1.0.12 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Closes #30.
PoN chunking:
pon_mutect2now runs per normal × scatter unit, using the same interval helpers asmutect2_call. The newpon_gather_vcfsGatherVcfs the chunks per normal into the unchanged{normal}.pon.vcf.gz, so GenomicsDB, CreateSomaticPanelOfNormals, combine and mask are untouched. On the APA cohort, the unscattered PoN step (20 whole-exome jobs) was the critical path.FreeBayes: bump 1.3.8 → 1.3.10 and pin vcflib 1.0.15. On the BIH HPC, 90 of 200
freebayes_callchunks (97 exomes) segfaulted with 1.3.8 + vcflib 1.0.12, invcflib::operator<<(ostream, Variant)(signal 11), and did so again on retry.🤖 Generated with Claude Code