bcftools norm --multialllelics -both v1.8 does not split FORMAT/AS_FilterStatus correctly
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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
- bioinformatics
Research direction
Reproduce the report with the supplied VCF record and bcftools norm -m -both, then compare the emitted records' AS_FilterStatus values with the input annotation. Start at the norm multiallelic-splitting entry point and verify that the value is separated on | rather than ,, with output matching the expected records.
Written by the indexing model from the issue text.
Description
hello，
In my vcf after splitting multiallelic sites, the info was separated wrongly,
like this
Before splitting
chrM 16189 . T C,A . PASS AS_FilterStatus=SITE|weak_evidence,base_qual,strand_bias,possible_numt; GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:3,2016,22:0.995,4.028e-03:2041:1,814,6:2,1101,3:0,3,659,1379
After splitting in bcftools norm -m -both mode
MT 16189 . T C . PASS AS_FilterStatus=SITE|weak_evidence; GT:AD:AF:DP:F1R2:F2R1:SB 0/1/0:3,2016:0.995:2041:1,814:2,1101:0,3,659,1379
MT 16189 . T A . PASS AS_FilterStatus=base_qual; GT:AD:AF:DP:F1R2:F2R1:SB 0/0/1:3,22:0.004028:2041:1,6:2,3:0,3,659,1379
Obviously, 'AS_FilterStatus' should be separated with '|',but it has been splitted by ','
So ,is there any solutions?
- Dominant language
- C
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- Merged PRs (30d)
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