Hello, I'm currently evaluating Funcotator from GATK v18.104.22.168. One of the annotations we are interested in is "variantClassification" (6th column in standard output). My understanding is this annotation utilizes the GENCODE GFF that is bundled with the data source package. I would like to be able and add transcript definitions from other sources, such as RefSeq, or maybe CCDS, in GTF or GFF format, and then receive back variantClassification strings based on these user-defined GTF/GFF data sources. Is this possible? If so, could you point me in the right direction?
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