How to filter out passed SNVs to create new files using bcftools isec.

Question

[addamyeo]

To specify from an earlier post, I need to filter out the passed SNVs, such that only the failed variants remain. The command I used to filter out the failed SNV is:

bcftools isec -f 'PASS,.' -e 'TYPE!="snp"' [file1.vcf.gz] [file2.vcf.gz] -p dir

Thanks!

[Pierre Lindenbaum]

dup of How to filter out failed SNVs to create new files using bcftools isec.