bcftools info and filter error
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]
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Ram
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SI_Genomics •
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SI_Genomics •
1 answer
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
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Pierre Lindenbaum
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