How to generate 'categ' field?


I'm working on somatic mutation dataset extracted from TCGA. To compute background mutation frequency (or rate), I need to classify each mutation into mutation categories. According to the introduction, catag can be computed based on {Variant_Classification, Reference_Allele, and Tumor_Seq_Allele1+2 columns}. In TCGA dataset (maf files), all of the fields are provided. However, I cannot fully understand how to compute it. Could you explain precisely?

I don't know why Broad has

I don't know why Broad has still not yet published exactly how this categ (especially in the context of creating the coverage file) is supposed to be computed.