I am trying to use FilterVcf (Picard) to filter out variant with AB<0.2 and AB>0.75 on my GATK vcf file. I saw that on FilterVcf documentation only have --MIN_AB parameter. Therefore, I cannot exclude variants with AB>0.75. Is there another software that can do this or do an annotation of AB on GATK vcf (because now there no AB annotation in GATK vcf)?
You can do that kind of operation with one-liners, they can be powerful when dealing with VCF files. See the example here) for MAF filtering on a homozygous species, you will need to adapt it for your own needs.