bcftools stats -s

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
38/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
bioinformatics, cli

Research direction

Reproduce the reported behavior with bcftools stats -s sample1,sample3,sample4... foo.vcf, using a VCF whose sample order includes the skipped sample. Start at the stats command's -s sample-selection handling; done means the reported statistics correspond to the requested sample names and order rather than the adjacent input samples.

Written by the indexing model from the issue text.

Description

needs-feedback

Hello,

I wanted to send a quick question regarding the bcftools stats function. If you ask for specific samples through 'bcftools stats -s; that is not in the exact order as provided in the vcf, it appears to provide the incorrect output. For examples, I was using bcftools stats -s sample1,sample3,sample4... foo.vcf (skipping sample2), and it provided an output with the same headers as the input (sample1,sample3,sample4), but the output were the stats of sample1,sample2,sample3. Thanks!

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

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