Problems with bcftools merge

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#1,915 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
Domain
bioinformatics, cli

Research direction

Start by reviewing the three attached VCF header excerpts and the bcftools merge behavior; the issue does not include the exact command or a reproducible error. Determine why the output contains fewer samples than expected, then document a reproducible diagnosis or the missing input requirements.

Written by the indexing model from the issue text.

Description

requires-test-case

Hi,
I'm having some problems with bcftools merge. In details, I can't merge three vcf files created with three different variant calling algorithms. Some vcf fields are different, and the code does not give me a clear error; however, when I open the resulting merged file, there are fewer merged samples than expected, and some vcf file are not included.
I attached the first lines of the three vcf files. I can't solve this problem.
Thank you in advance for your help and time,

Paola
sample3.txt
sample2.txt
sample1.txt

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

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