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single sample VCF - add flag to FILTER based on AF in genotype
I am trying to either hard filter or flag variants where the AF < 0.05. The VCF was generated using MUTECT2 in GATK220.127.116.11. The VCF is a single sample VCF, and does not have 'AF' in the INFO field. It does have AF in the FORMAT field. I did try using VariantFiltration with --genotype-filter-expression "AF < 0.05" --genotype-filter-name "MAF<5%", but I have sinced learnt that this does not add a flag to the FILTER field. Any help appreciated.