I use bcftools norm to split and left-normalize variants (like the line in file). After norm the variant is split correctly and annotated, my question is can the AF tag be used to filter out AF= below 20% in the command or is there another? So in this case the first split vatiant is filtered out. Thank you :).


    before bcftools norm
    chr4	187004216	.	TC	T,TT

    after bcftools norm
    chr4	187004217	187004217	C	-
    AF=0.0305344;AO=130
    chr4	187004217	187004217	C	T
    AF=0.969466;AO=673

    desired output
    chr4	187004217	187004217	C	T
    AF=0.969466;AO=673
You are certainly correct to normalise the file prior to filtering; otherwise, you would obtain unexpected results.

To filter on AF, use `bcftools view`, specifically the following parameters:

> -q/Q, --min-af/--max-af

Kevin