Where to download latest TCGA MAF files?

Question

[ckr123]

According to Broad Institute Firehose, there are four latest MAF files:

bcm.edu        214  214  140005  hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.1.somatic.maf.txt        38.6MB  14-Apr-15
bcm.edu        53   53   10986   hgsc.bcm.edu_COAD.SOLiD_DNASeq.1.somatic.maf.txt             3.4MB   24-Mar-15
bcm.edu        53   53   11578   hgsc.bcm.edu-COAD-from-BCM-Firehose-CRC-08nov11.maf.txt      2.8MB   18-Dec-12
broad.mit.edu  102  102  48984   broad.mit.edu_COAD.IlluminaGA_DNASeq.1.somatic.maf.txt       12.3MB  14-Apr-15
broad.mit.edu  102  102  50982   hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.1.broad.mit.edu.maf.txt  12.8MB  23-Jul-12

Three of the five files were modified on 2015, but when I tried to locate these files on NCI and TCGA data portal, the latest files were still from 2013. Any idea about where to find the 2015 files?

MAF File Name                                      Tumor Samples:Normal Samples  MAF Version  Archive Name                                       Deploy Date
hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.1.somatic.maf  220:221                       version 2.4  hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.Level_2.1.5.0  18-Jun-13
hgsc.bcm.edu_COAD.SOLiD_DNASeq.1.somatic.maf       53:53:00                      version 2.4  hgsc.bcm.edu_COAD.SOLiD_DNASeq.Level_2.1.7.0       30-Jul-13

MAF File Name                                      Tumor Samples:Normal Samples  MAF Version  Archive Name                                       Deploy Date
hgsc.bcm.edu_READ.IlluminaGA_DNASeq.1.somatic.maf  81:81                         version 2.4  hgsc.bcm.edu_READ.IlluminaGA_DNASeq.Level_2.1.6.0  18-Jun-13
hgsc.bcm.edu_READ.SOLiD_DNASeq.1.somatic.maf       35:35:00                      version 2.4  hgsc.bcm.edu_READ.SOLiD_DNASeq.Level_2.1.7.0       30-Jul-13

Answer 1

[michael.d.mclellan]

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".

[-_-]

Do you know the difference between Mutation_Packager_Calls and Mutation_Packager_Oncotated_Calls, please?

Answer 2

[Maarten Slagter]

This page should list all the latest MAF files

This page contains derived somatic MAF files