Question: Consolidated MAF file for all cancers in TCGA
gravatar for somy.ork
3.2 years ago by
somy.ork0 wrote:


I want a consolidated MAF file for all cancers from TCGA data.

Is it correct to use the MAF search tool:

Click all in the left side panel and create and custom maf download and use it?

From this link:

I see a list of files they have chosen for the tool is from all cancers and similar files are being used by broad at firehose and TCGA Pancancer analysis.



But I am surprised that I never across in any of the TCGA MAF discussions in this forum about the topic of 'custom data exported from MAF search tool'. Can anyone explain this?



snp forum • 1.2k views
ADD COMMENTlink modified 2.9 years ago by genomax64k • written 3.2 years ago by somy.ork0
gravatar for michael.d.mclellan
2.9 years ago by
United States
michael.d.mclellan140 wrote:

Firehose now 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 2.9 years ago by michael.d.mclellan140
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