VCF parse error:FILTER ' PASS' is not defined in the header
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 20/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics, cli
Research direction
No repository file or test is named in the report. Reproduce the command bcftools view white_yakXcow.FI.vcf -Oz -o white_yakXcow.FI.vcf.gz with the supplied VCF, then inspect the FILTER header entries and the value reported as ' PASS'; done should be a confirmed parser diagnosis and a documented expected behavior or fix.
Written by the indexing model from the issue text.
Description
Dear all,
I 'm compressing vcf with the following code:
bcftools view white_yakXcow.FI.vcf -Oz -o white_yakXcow.FI.vcf.gz
The input white_yakXcow.FI.vcf is like
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
##FILTER=<ID=filtered,Description="QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > ### 3.0">
and I got the error
[W::vcf_parse] FILTER ' PASS' is not defined in the header
[E::vcf_parse] Could not add dummy header for FILTER ' PASS'
Error: VCF parse error
- Dominant language
- C
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- 2d 23h
- Merged PRs (30d)
- 2
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