Question: Are the somatic mutations in TCGA filtered for germline mutations?
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gravatar for rafi.zon
19 months ago by
rafi.zon10
rafi.zon10 wrote:

Hi, I read from somewhere an answer Question: How do I get germline mutation data from TCGA that the germline mutations are filtered from the somatic mutations in the MAF of open access data in TCGA.
Is this truly the case?
Another possibility could be that the somatic mutations are detected with respect to a reference genome and thus include the germline mutations of a considered patient. Anyone with experience on this matter?

filtering mutations tcga • 760 views
ADD COMMENTlink modified 19 months ago by markus.riester500 • written 19 months ago by rafi.zon10
1
gravatar for markus.riester
19 months ago by
markus.riester500 wrote:

They sequenced matched normals, so yes, it is the case. Have a look at the detailed papers associated with each TCGA dataset.

ADD COMMENTlink written 19 months ago by markus.riester500

Didn't know they have a paper for each dataset. Will have a look, thanks.

ADD REPLYlink modified 19 months ago • written 19 months ago by rafi.zon10
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