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GATK 4.0.4.0 Mutect2 - filtering multialleleic calls

mbyvcmmbyvcm Member
edited September 2018 in Ask the GATK team

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.

Thanks
Chris

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