after gatk merge gvcf to vcf; then bcftools stats, I found a result of stats lose some count

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
data

Research direction

Start by reproducing the example through bcftools stats using the shown VCF record, after the GATK gVCF-to-VCF merge. Trace how the A,* alternate alleles are classified and compare the reported indel count with the expected count; done means the relevant stats output counts this case consistently.

Written by the indexing model from the issue text.

Description

needs-feedback

as like title, if one line like this "chr1 11140624 . C A,* 366.64 . AC=1,1;AF=0.250,0.250;AN=4;BaseQRankSum=-8..." , in "A,*", symbol star indicate there is one sample lose REF C, So I think this line should increment indel counter, But actually Not, could you fix this problem? Thankyou

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

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