Dear GATK team
I there a way to include the "FILTER" column (from the output of FilterMutectCalls) in the output of Funcotator? I can see that all the "INFO" data is included, however "FILTER" content seem to be missing in the Funcotator output.
I know about the option "--remove-filtered-variants", which works fine, but I would like to not only include those variants that get "PASS" but also check on some others, e.g. germline_risk.
I run Funcotator with the somatic data source, read in a vcf, output a maf, GATK version 220.127.116.11.
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