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:
> 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
> 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
> '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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