bcftools view -R is excluding regions in bed file

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics, cli

Research direction

Start by reproducing bcftools view -R regions.bed input.vcf.gz with the reported BED and VCF inputs, then compare the selected variants with the regions in regions.bed. Check the bcftools view -R entry point and its documented region-coordinate behavior; done means determining whether the result is a bug or an input/usage issue and adding the appropriate regression coverage or clarification.

Written by the indexing model from the issue text.

Description

requires-test-case

Hi,

I am using bcftools view -R regions.bed input.vcf.gz to extract only those variants present in regions.bed. However, I get only those variants not present in regions.bed, so exactly the opposite. I really don't know what is going on... Any help?

Thanks!

Anna

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

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