bcftools merge changing the alleles

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start by reproducing the reported bcftools merge -m id command with file1.vcf.gz and file2.vcf.gz, comparing the input and output allele strings. Trace the merge path responsible for allele handling and add a regression test using the reported multi-allelic marker; done means merging preserves the complete allele sequences.

Written by the indexing model from the issue text.

Description

enhancement

Command:
bcftools merge -m id file1.vcf.gz file2.vcf.gz -O z -o output.vcf.gz

For one of the multi-allelic markers, alleles in file1 and file2:
CGAATGGAATGGAATGGAAT CGAATGGAATGGAAT,CAAATGGAATGGAATGGAAT,CGAATGGAATCGAATGGAAT,CGAATGGAATTGAATGGAAT

Alleles in output:
CGAATGGAATG CGAATG,CAAATGGAATG,CGAATGGAATC,CGAATGGAATT
(i.e. it is stripping down the alleles)

File1 and file 2 do not have overlapping samples. Any help with this?

Dominant language
C
Stars
891
Forks
277
Avg merge
2d 23h
Merged PRs (30d)
2

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