Download all DNA mutations from TCGA

Question

[ceruleanivy]

I would like to download all the available TCGA data on mutations for colon adenocarcinoma, including every sample that was tested under this multi-institutional endeavor, but I cannot figure out how to find the desired information. By visiting the 'searchForTCGAData' page and selecting Data Catgegory: DNA mutation and Disease: COAD I get 384 different results. Do these files correspond to different patients/samples ?

[chen]

I think you can download all TCGA vcf files and parse them by yourself.

Answer 1

[igor]

I personally find Broad GDAC Firehose to be the easiest way to access TCGA data, especially if you want it combined: http://gdac.broadinstitute.org/runs/stddata__latest/

Update: UCSC Xena seems to be even better organized and contains more recent data: https://xenabrowser.net/datapages/

Answer 2

[Chris Miller]

You can download the somatic variants in MAF format here: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/gsc/hgsc.bcm.edu/illuminaga_dnaseq/mutations/hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.Level_2.1.5.0/hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.1.somatic.maf

[steve]

Looks like this URL is no longer working

[glocke01]

try https://portal.gdc.cancer.gov/repository

[ceruleanivy]

Thanks! May I ask how did you search in order to find the file above ? By using File Search as a method -->DNA mutation, COAD, Open Access I get two files other than descriptions rather than one.

[Chris Miller]

I usually go straight to the data directories (i.e. https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/) and click through from there until I get the file I need.