Trim unsupported alleles off the sites filterAC0 keeps - #1982
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glennhickey wants to merge 2 commits into
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Trim unsupported alleles off the sites filterAC0 keeps#1982glennhickey wants to merge 2 commits into
glennhickey wants to merge 2 commits into
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filterAC0 is a record-level filter: `bcftools view -e MAX(AC)=0` decides whether to emit a row, never what is in it. So a bubble carrying 200 traversals of which one is genotyped comes through with all 200 alleles and all 200 AT strings attached. Dropping the whole site instead is what the plain `AC=0` form used to do, and that was worse -- the point here is that neither end of the record-level choice is what the option is for. Add `bcftools view -a` behind it. vg declares AC/AF Number=A and AT Number=R, so bcftools subsets all three in step with ALT and renumbers the GT indices; AN and NS need no fixup pass, since trimming changes which alleles ALT lists, not which samples are called. Order is load-bearing. `-a` first would trim every allele off a site nothing carries, leaving ALT=. with no AC at all, and MAX(AC)=0 does not match a missing tag -- the empty record would then survive the filter that exists to remove it. chunked_vcfwave is deliberately untouched: it runs `norm -m -any` ahead of its own AC=0, so the split already makes that a per-allele decision. .raw.vcf.gz never goes through vcfbub() and still keeps every traversal. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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filterAC0 is a record-level filter:
bcftools view -e MAX(AC)=0decides whether to emit a row, never what is in it. So a bubble carrying 200 traversals of which one is genotyped comes through with all 200 alleles and all 200 AT strings attached. Dropping the whole site instead is what the plainAC=0form used to do, and that was worse -- the point here is that neither end of the record-level choice is what the option is for.Add
bcftools view -abehind it. vg declares AC/AF Number=A and AT Number=R, so bcftools subsets all three in step with ALT and renumbers the GT indices; AN and NS need no fixup pass, since trimming changes which alleles ALT lists, not which samples are called.Order is load-bearing.
-afirst would trim every allele off a site nothing carries, leaving ALT=. with no AC at all, and MAX(AC)=0 does not match a missing tag -- the empty record would then survive the filter that exists to remove it.chunked_vcfwave is deliberately untouched: it runs
norm -m -anyahead of its own AC=0, so the split already makes that a per-allele decision. .raw.vcf.gz never goes through vcfbub() and still keeps every traversal.