There are multiple reasons that could contribute to an instance in which harmonized tumor and normal BAM files for a specific case are available but the variant calls are not. The two most common reasons are as follows:
GENCODE gene sets are continuously updated to improve the coverage and accuracy. GENCODE 36, which was released in October of 2020, includes many updates to definitions of genes, transcripts, long non-coding RNAs, and other types of annotations. The previous version used by the GDC (GENCODE 22) was released in March 2015. Both versions were built on Ensembl genome assembly GRCh38.
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