[GDAC-users] Re: TCGA Coverage Data

Subject:   [GDAC-users] Re: TCGA Coverage Data (more for this subject)
From:   David Heiman <> (more from this sender)
Date:   Oct 20, 2015 12:04

Hi Perry,
My understanding is the publicly available data is generated by whole exome  
sequencing, so there is no publicly available broader coverage data. There  
are some cases of whole genome sequencing, but I believe access to those  
requires dbGAP credentials. Also, not all centers use MuTect, nor do they  
all submit coverage files.
On Saturday, October 17, 2015 at 1:48:28 PM UTC-4, Perry Palmedo Jr wrote:
> Hi,
> 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  
> <https://www.google.com/url?q=https%3A%2F%2Fwww.broadinstitute.org%2Fcancer%2Fcga%2Fmutsig_run&sa=D&sntz=1&usg=AFQjCNE5AlZ5FYqZTVssZaM65l456By1dQ&gt;)  
> 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)?
> Thanks!
> Perry Palmedo
To unsubscribe from this group and stop receiving emails from it, send an email to .