CGC mutation data not matching downloadable maf
Dear CGC team,
When I compare the mutation data I download from the TCGA website (maf files), they don't match up with the data displayed in CGC. For example, in ovarian cancer 8% and 9% of patients are BRCA1 and BRCA2 mutated. When I pull these data up in the browser, there are only 2 BRCA2 mutations showing up. The same pattern is true for TCGA LUSC and BLCA, with CGC displaying fewer mutations than shown in the raw data. Can you please explain this discrepancy?