Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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 GATK18.104.22.168. 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.