Hy everyone,
my question is: if a TCGA sample there is not in the MAF file for specific gene mutations (ex. KRAS), this means that patient not have KRAS mutations or that the patient was not analyzed in the corresponding pipeline?
Thank you!
MAF files contain only "positive" data. Lack of a mutation may mean that the patient did not have a mutation (true negative), was not tested for that mutation (panel did not cover the gene/location of interest), the mutation was "present" but filtered out in post-processing, or that the mutation was a false negative and not detected. Determining which of these cases applies can be challenging without information about read depth and potentially read counts for each allele at a "negative" site.
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version 2.3.6
From where did you obtain the MAF file? - please be very specific. The TCGA samples were processed at different institutes / centres, and each would have produced a separate MAF file. If a patient's mutation data is not in one MAF file, it may be in another that you need to download.