feat: implement somatic SNV/indel benchmarking pipeline - #1

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apsteinberg wants to merge 13 commits into

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Commits on Jun 9, 2026

initial commit for per sample query/truth strategy and stratification of statistics by challenging genomic regions
apsteinberg
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1f69723
test workflow
apsteinberg
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d4d7251
add docker images for the aggregation and stats steps
apsteinberg
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2a622ca
precommit linting
apsteinberg
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4049e2b
ignore nf-test content in linting
apsteinberg
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8f98cb3
allow for different sample names when concatenating truth vcfs
apsteinberg
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2127cd9
reheader vcfs from the same sample to fix downstream bcftools concat issue
apsteinberg
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df5a1cc
carry through tabix indices
apsteinberg
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c34376e
fix: BCFTOOLS_VIEW tuple arity for Nextflow 26 compatibility
apsteinberg
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f7a9aea

Commits on Jun 10, 2026

add additional stats to stratification output
apsteinberg
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517f552

Commits on Jun 11, 2026

remove truth_qual column (Illumina somatic VCFs have no QUAL)
apsteinberg
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0873ee5
feat: add consensus truth strategy (>=2/N agreement via bcftools isec)
apsteinberg
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d3056b0
linting
apsteinberg
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5841232