Issue in merging several vcfs

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#1,419 3 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics, cli

Research direction

Start with the reported bcftools merge command and the 100 compressed, indexed VCF inputs, then determine why the process is being killed. Done means identifying a reproducible cause or limitation and documenting a supported way to complete the merge.

Written by the indexing model from the issue text.

Description

needs-feedback

Hi,
I installed bcftools and I ran bgzip and indexed the files using following commands.
bgzip -c file1.vcf > file1.vcf.gz
bcftools index file1.vcf.gz

However, once I merged using following command, terminal shows "killed". I have total 100 vcfs.
bcftools merge ls *.vcf.gz -O v > merged.vcf

Please advise how to overcome.

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

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