I have a multi-sample VCF generated by GATK with an additional 'Allele fraction' (AF) annotation in the FORMAT field.
I wish to filter the SNPs in the VCF at the sample genotype-level using the AF in the FORMAT field and I want to remove sites with missing values (".") but without removing the whole variant.
I have tried the command GATK SelectVariant --select 'vc.hasAttribute("AF")' but that doesn't work.
Does anyone know of a simple way or a tool that could accomplish this?
Suggestions highly appreciated!