[GDAC-users] TCGA Coverage Data

Subject:   [GDAC-users] TCGA Coverage Data (more for this subject)
From:   Perry Palmedo Jr <> (more from this sender)
Date:   Oct 16, 2015 14:52

I am a graduate student in Bonnie Berger's lab. I am looking to get access
to coverage files for TCGA data. I am interested in the WIG files from
MuTect, however there seem to be inconsistencies in the publicly available
data. For all of the publicly available data on Firehose it seems like the
coverage data has been filtered to only include exons. Where can I get the
broader coverage data?
The MutSig example data (LUSC from
https://www.broadinstitute.org/cancer/cga/mutsig_run) includes non-coding
calls in the MAF that are not in the Firehose MAF for LUSC, but the
coverage file is only at the gene level. When I look at the coverage data
on Firehose, it does not include introns. I also looked at the coverage
data on Synapse, and this appears to match the coverage data on Firehose.
Is there some way to access the complete WIG files for this data?
Ultimately I need the full coverage regions where mutations could have been
called. Any help is much appreciated.
Additionally, https://www.broadinstitute.org/cancer/cga/mutsig_run has a
'exome_full192.coverage' file. Is there documentation or someone that can
tell me exactly how this file was generated (i.e. what annotation procedure
was used)?
Perry Palmedo
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