I want to extract all somatic mutations from TCGA vcf files, I have three sources for each file: samtools-Sniper-VarscanSomatic; and for each one I have a normal and mutated sample column. can i applay varscan commands?
You can start with VCF2MAF. You can alter the code to output whatever you want. It also adds VEP annotation
Converting Vcf File To Maf C: Vcf To Maf (Mutation Annotation Format) Conversion ? http://seqanswers.com/forums/showthread.php?t=16740
Please note that various curated MAFs for each TCGA project are freely available Open Access Data
In addition, Firehose hosts the latest "recommended" MAF for each TCGA tumor type.
To retrieve these:
$ wget http://gdac.broadinstitute.org/runs/code/firehose_get_latest.zip $ unzip firehose_get_latest.zip ./firehose_get -b -only Mutation_Packager_Oncotated_Raw_Calls Mutation_Packager_Oncotated_Calls data latest
For each tumor type, use "Mutation_Packager_Oncotated_Raw_Calls" if available. If not, then use "Mutation_Packager_Oncotated_Calls".