I would need to filter VEP annotated vcf file and find all variants where gnomADe_AF < 0.001.
bcftool query -I 'gnomADe_AF<0.001' -f '%CHROM %INFO/gnomADe_AF\n' file.vcf.annotated does not return anything or even give any errors.
If I put
bcftool query -I 'AF<1' -f '%CHROM %INFO/AF\n' file.vcf.annotated the command works and I get all variants with AF<1. And in the headers I checked that there is gnomAD_AF and AF in the INFO tags.
Could anyone help with how to filter this with unix?
EDIT: I can see the values for gnomADe_AF when looking with less, but for some reason I can't get them with any commands separately.