bcftools info and filter error

Question

[SI_Genomics]

Hi. I am trying to do a comparative analysis of my vcf file against the vcf files of ExAc. I'm using the bcftool isec here. I am getting an error that says:

[W::vcf_parse_info] INFO 'HOM_CONSANGUINEOUS' is not defined in the header, assuming Type=String
[W::vcf_parse_filter] FILTER 'AC_Adj0_Filter' is not defined in the header

I'm not sure how to annotate the header and resolve this. [I'm an amateur in this with very rudimentary knowledge of programming]

Answer 1

[Pierre Lindenbaum]

use awk to insert a filter defintion in the VCF

awk '/^#CHROM/ {printf("##FILTER=<ID=HOM_CONSANGUINEOUS,Description=\"blabla\">\n##FILTER=<ID=AC_Adj0_Filter,Description=\"blabla\">\n");} {print}'  in.vcf