Consolidated MAF file for all cancers in TCGA

Question

[somy.ork]

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+Dashboard

https://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?

Answer 1

[michael.d.mclellan]

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.