GATK 18.104.22.168 Mutect2 - filtering multialleleic calls
I want to remove positions from my VCF which have more than one alternative allele in the ALT field. At most sites with multiple ALT calls, mutect2 has added the 'multialleleic' FILTER. However, there are some sites where this flag is not applied:
1 16959732 . T TGGGCCCGCAGCA,TGGGCCTGCAGCA . PASS
19 31611623 . GA G,AA . PASS
Ultimately I am trying filter my VCF by "AF" - which GATK VariantFiltration will not let me do if there are multiple values for AF as a result of multiple alternate alleles.