I am seeing discrepancies between the cBioPortal and the number of mutations from the GENIE MAF file. For instance, for prostate cancer metastasis samples, from the MAF file, I?m seeing 15 mutations, but on cBioPortal, I see 10 (excluding deep deletions and fusions, assuming those aren?t in the MAF files). Are there types of SNPs that aren?t in cBioPortal which explains the difference?
Created by Sara Selitsky selitsky Dear @selitsky ,
Sorry for the delay in response. All variant data is provided to cBioPortal.
If you are seeing a discrepancy, please provide the GENIE data version number and the specific oncotree codes so we can take a look.