Incorrect allele ("2") in... when trying to merge, merged files

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Quiet
Tech stack
c
Domain
bioinformatics

Research direction

The report names bcftools 1.21 and two merged, compressed, indexed VCFs; start by reproducing the second merge and inspect chr1:939414 for sample CC0037_CC0037_N. Determine whether merging the intermediate files reliably causes the incorrect-allele error and document the conditions or input issue found.

Written by the indexing model from the issue text.

Description

requires-test-case

bcftools version 1.21

I have about 230 massive vcfs that I am trying to slap together. I kept crashing everything while merging all 230 at once, but I managed to get them merged, zipped, and indexed in two batches. I then wanted to merge the two merged vcf.gz files. However, I ran into an error:

[E::bcf_calc_ac] Incorrect allele ("2") in CC0037_CC0037_N at chr1:939414

which I thought was interesting as these samples have already been merged just fine? Not sure if merging already merged files is a problem or if some sort of artifacting is happening.

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

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