VCF parse error:FILTER ' PASS' is not defined in the header

samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

http://samtools.github.io/bcftools/

Other

657 stars 240 forks source link

VCF parse error:FILTER ' PASS' is not defined in the header #1762

Open wzp99 opened 2 years ago

wzp99 commented 2 years ago

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=

ALT=

FILTER=

FILTER= 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

pd3 commented 2 years ago

Any chance you could share a part of the VCF with me to reproduce the problem locally?