Are the somatic mutations in TCGA filtered for germline mutations?
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2.2 years ago
rafi.zon ▴ 10

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?

tcga mutations filtering • 922 views
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2.2 years ago

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

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

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