How to get somatic variant from TCGA vcf files

Question

[Lynda lyn]

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?

Answer 1

[michael.d.mclellan]

You can start with VCF2MAF. You can alter the code to output whatever you want. It also adds VEP annotation

https://github.com/ckandoth/vcf2maf

Related threads:

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

    https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/

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".

[Shicheng Guo]

This link is broken: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ Maybe you can update it.