Good afternoon,

I'm trying to filter a VCF file that has the following dummy flag values:

• PASS: All filters passed
• Fa: Failed filter a
• Fb: Failed filter b
• Fc: Failed filter c
• Fd: Faield filter d

Variants can fail one or more filters. Variants that fail multiple filters will be annotated with the corresponding flags separated by semi-colon. Thus, the filter column can have one of the 5 above values, or any number of F* values separated by ;.

I'd like to select all variants that either PASSed or only failed filter a. How can I do this in bcftools? The -f option skips location that does not contain one of the listed filters, so it keeps locations that contain any of the listed filters. When I use

bcftools view -f PASS,Fa ...

I get rows that failed filter a along with other filters also. That is, the above expression matches both Fa and Fa;Fb. I tried excluding the delimiter, but that didn't work:

bcftools view -f 'PASS,Fa,;' ... #didn't work

Does anyone know how to exclude or include exactly a list of filters? Nothing in the -i or -e EXPRESSIONS is useful either.

This is what I'm using right now, which is awk mocking bcftools:

zcat vcf_file.vcf.gz | awk -F"\t" -vOFS="\t" '$0 ~ /^#/ {print} $7=="PASS" || $7=="Fa" {print}'