Question: How to get somatic variant from TCGA vcf files
gravatar for Lynda lyn
4.0 years ago by
Lynda lyn30
Lynda lyn30 wrote:

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?

somatic mutations vcf • 3.1k views
ADD COMMENTlink modified 3.9 years ago by michael.d.mclellan150 • written 4.0 years ago by Lynda lyn30
gravatar for michael.d.mclellan
3.9 years ago by
United States
michael.d.mclellan150 wrote:

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

Related threads:

Converting Vcf File To Maf
C: Vcf To Maf (Mutation Annotation Format) Conversion ?

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 $ unzip ./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".

ADD COMMENTlink written 3.9 years ago by michael.d.mclellan150

This link is broken: Maybe you can update it.

ADD REPLYlink written 3.0 years ago by Shicheng Guo8.1k
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