Within the GDC data analysis workflow, both public (somatic) MAFs and protected MAFs generated are from the same pipeline and link back to the same cases. For example, For the TCGA-GBM project, the somatic MAF has the following header:
# in TCGA.GBM.muse.7e85de23-3855-4279-a3ac-a81827e4ccb6.DR6.0.somatic.maf.gz
#version gdc-1.0.0
#filedate 20170307
#n.analyzed.samples 393
In general, n.analyzed.samples is used as a denominator to calculate mutation frequencies. If no variants for a case passed our filters, the case should still be counted; however, if the case was determined to have poor quality (such as for high contamination, duplicates etc.), it is not counted in the public MAF. In this particular project (TCGA-GBM), there were 396 cases with SNV data. Our analysis pipeline revealed that among them, a total of 5 GBM tumor aliquots had high contamination. Among these 5 patient, 2 had another good tumor aliquot, but 3 had only one aliquot. As the result, those 3 cases were removed from the public MAF.