'bcftools call' should output SNP/INDEL of same site to one vcf record
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by reproducing the report from a.zip with bcftools call, then run the shown bcftools norm -m+any and bcftools plugin fill-AN-AC pipeline to inspect the inconsistent FORMAT/GT values. Trace the bcftools call entry point and its handling of SNP/INDEL records at one site; done means the variants are emitted as one VCF record with consistent genotype information.
Written by the indexing model from the issue text.
Description
'bcftools call' should output the SNP/INDEL of same site to one vcf record.
Now the SNP/INDEL of same site are output separately, and sometimes the FORMAT/GT info of two record are inconsistent.
If we 'bcftools norm -m+any a.vcf | bcftools plugin fill-AN-AC', we can find this inconsistent in GT.
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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