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?
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.