Question: Consolidated MAF file for all cancers in TCGA
0
gravatar for somy.ork
3.7 years ago by
somy.ork0
somy.ork0 wrote:

Hi

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

Is it correct to use the MAF search tool: https://tcga-data.nci.nih.gov/search/#/

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

From this link: https://wiki.nci.nih.gov/display/TCGA/Publication+MAF+Search+Input

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.

https://confluence.broadinstitute.org/display/GDAC/MAF+Dashboardhttps:

//docs.google.com/spreadsheets/d/18SS7g6P8QCRL-2uDKS0uvVt_2O9YbtfMcy_ep_SWCus/edit?pref=2&pli=1#gid=2

 

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 • 1.4k views
ADD COMMENTlink modified 3.4 years ago by genomax71k • written 3.7 years ago by somy.ork0
1
gravatar for michael.d.mclellan
3.4 years ago by
United States
michael.d.mclellan150 wrote:

Firehose now 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".

ADD COMMENTlink written 3.4 years ago by michael.d.mclellan150
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