could not parse the input VCF
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
Start by reproducing the shown bcftools mpileup | bcftools call pipeline and inspect the generated VCF header alongside the reported INFO, contig, and FILTER warnings. Compare the header and contigs with hg38.fa, then rerun the command; done means the output VCF parses without these errors.
Written by the indexing model from the issue text.
Description
Hi,
I want to call SNPs for PacBio HiFi assembled haplotype genome using the following command:
bcftools mpileup -f hg38.fa --threads 16 -O v $file | bcftools call --ploidy 1 -mv -o ../SNP/$vcf
The following information was reported:
[mpileup] maximum number of reads per input file set to -d 250
[W::vcf_parse_info] INFO 'MQ0' is not defined in the header, assuming Type=String
Error: could not parse the input VCF
[mpileup] maximum number of reads per input file set to -d 250
[W::vcf_parse] Contig 'chrUn_KI270' is not defined in the header. (Quick workaround: index the file with tabix.)
Error: could not parse the input VCF
[mpileup] maximum number of reads per input file set to -d 250
[W::vcf_parse_filter] FILTER '' is not defined in the header
Error: could not parse the input VCF
The contigs were mapped to hg38 using minimap2:
minimap2 -t 12 -ax asm5 hg38.fa ./assemble/$file > ./AlignedSam/$out
I tried to restart some failure programe and recived complete SNP files.
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- Merged PRs (30d)
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