When I run this command:
bcftools view -i 'F_PASS(GT!="mis")>0.9' <file.vcf.gz>
I get this error:
Error: the tag "F_PASS" is not defined in the VCF header
My command seems to follow the syntax in the example on this page: samtools.github.io/bcftools/bcftools.html where it is stated as
F_PASS(GQ>90 & GT!="mis") > 0.9.
The only difference I can see is that I have removed the
GQ>90 & part, which still makes sense syntactically.
Why would bcftools view mistake a (boolean) command for a file header?