Using COUNT with bcftools filter across all samples

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics, cli

Research direction

Start by reading the bcftools filter expression documentation for COUNT and FORMAT sample indexing, then reproduce the example command with a multi-sample VCF. Determine whether the requested all-sample count is already expressible; done means documenting the supported syntax or defining the required behavior and tests.

Written by the indexing model from the issue text.

Description

Is there a way to use bcftools filter with COUNT to return only positions with a certain number of values for a given FORMAT entry across all samples?

For example, I'd like to filter out positions where the number of all AD values is exactly two. I can do this for one sample, like this:

bcftools filter -i 'COUNT(AD[0:*]) == 2' input.vcf.gz > filtered.vcf

Is there a way to do this for all samples? Or do I have to enter each position manually? I've tried various permutations of the indexing syntax but it doesn't quite seem to do what I need.

thanks!

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

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