feature request: polyploid variant calling

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
25/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Review the existing bcftools mpileup | bcftools call pipeline and clarify the intended polyploid variant-calling behavior and supported ploidy levels. No source files, tests, or acceptance criteria are named; done would require an agreed implementation scope and validation criteria.

Written by the indexing model from the issue text.

Description

Dear bcftools team,

this was brought up in a chat with @pd3 about a month ago — it would be cool to be able to call variants at ploidy levels above 2 with the bcftools mpileup | bcftools call pipeline! I am aware of freebayes and gatk but I got to like bcftools variant calls for their balance of sensitivity and not too heavy assumptions of the input data which altogether works well for non-human population datasets. Is that something that is on the roadmap or at least feasible to implement?

Cheers, Nikita

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

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