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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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Wrong case in VCF file - REF vs Ref and missing q10 #64

Closed tseemann closed 3 years ago

tseemann commented 4 years ago 
##FILTER=<ID=Ref,Description="Genotyping model thinks this site is reference.">
##FILTER=<ID=BreakPoint,Description="It is predicted as a breakpoint">
##FILTER=<ID=DUP,Description="Duplicated regions(>=50bp).">

  1. In the VCF you use "REF" not "Ref"

  2. In the VCF you use "q10" but there is no q10 in VCF header above

[W::vcf_parse] FILTER 'REF' is not defined in the header
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
  1. Missing defintion of DP ?
hsinnan75 commented 4 years ago

Thank you for pointing our those issues, I'll fix them.

hsinnan75 commented 4 years ago

I've fixed the REF and q10 in VCF header. And I also defined INFO 'DP' in the header. Thank you for pointing out those issues.