I am struggling with selection of maf files for mutation analyses on TCGA patients. Here is the actual problem.
Say I want to do somatic mutation analysis for GBM patients. So there are two types I can get the data from
(i) From TCGA-DATA MATRIX (https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm), I selected 'somatic mutations' in "Data Type" and clicking apply I followed the email link to download the data. By untarring the file I got Level_2 maf file named "broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2.maf" having 21495 lines (first line being the header)
(ii) From broad institute 's "MAF+Dashboard" facility (https://confluence.broadinstitute.org/display/GDAC/MAF+Dashboard) I got two files for GBM tissue under the main section (MAFs Available from the DCC as of 26 February 2015) of this above said web link page.
these two files are:
(a) gbm_liftover.aggregated.capture.tcga.uuid.somatic.maf (22169 lines )
(b) step4_gbm_liftover.aggregated.capture.tcga.uuid.maf2.4.migrated.somatic.maf (22171 lines)
Now my confusion is, which file to proceed with for mutational analysis in GBM.
thanks in advance.