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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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norm doesn't normalize <DUP> symbolic variants #2145

Closed davmlaw closed 2 months ago

davmlaw commented 3 months ago

I raised an issue as #1919 "norm doesn't normalize symbolic variants" but it was closed after only fixing <DEL> - so there's no open issue for all of the other symbolic variants which are still affected.

<DUP> is the next most common indel I guess so I've attached a normal VCF (which is normalized) and a symbolic representation of the same variant (which is not) as a test case:

bcftools_norm.zip

bcftools norm norm_dup_grch38.vcf -f /data/annotation/fasta/GCF_000001405.39_GRCh38.p13_genomic.fna.gz

The explicit alt one gets left aligned:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
NC_000001.11    117395877   .   G   GGATTACA    .   PASS    .
Lines   total/split/realigned/skipped:  1/0/1/0
pd3 commented 2 months ago

This is now supported.