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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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VCF headers missing 3 things #32

Closed tseemann closed 4 years ago

tseemann commented 4 years ago 
bcftools  filter -i 'FILTER="PASS"' output.vcf

[E::bcf_hdr_parse_line] Could not parse the header line: "##CommandLine=<MapCaller -i /genome -ad 3 -ploidy 1 -t 16 -vcf raw.vcf -f R1.fq.gz -f2 R2.fq.gz>"

[W::vcf_parse] INFO 'END' is not defined in the header, assuming Type=String

[W::vcf_parse] Contig 'Chromosome' is not defined in the header.

  1. I think you need to remove the < ..... > from the ##CommandLine

  2. Need to add ##INFO=<ID=END definition

  3. Need to add contig headers - can you get them from the -i bwtindex file?

    ##contig=<ID=contig00001,length=124664>
##contig=<ID=contig0383,length=6243596>
hsinnan75 commented 4 years ago

Thank you! I've fixed those errors. (v0.9.9.15)

tseemann commented 4 years ago

Looks good!