I have access to controlled data. I have done this some years ago, but can't seem to figure out the new interface. Ideas?
Hi Eitan
Indeed, the TCGA website has been taken offline and combined to GCD, so you should use the GDC website.
I spoke to Vesteinn Thorsson, who worked on TCGA and the Cancer Genome Cloud (CGC). He said Reyhaneh's answer is correct, as far as it goes: you should use the GDC website. However, he also points out that there isn't much germline data available. To be quite honest, he said "Good luck...and you can quote me on that."
Sorry to be the bearer of bad news!
Just a flash thought. The TCGA consortium makes available a little set of healthy-matched, in general "control", samples for each tumor type. In your place, I'd download the FASTQ files corresponding to these pairs and would run a "paired" variant call pipeline, like the one provided by VarScan or MuTect (below, a detailed list of similar tools).
The results of MuTect, for example, contain all variants (those discarded from the tumor sample and thus likely germline, beucase somehow present also in the paired control sample) and just the ones predicted to be somatic.
http://varscan.sourceforge.net/
https://www.biostars.org/p/19104/
http://archive.broadinstitute.org/cancer/cga/mutect
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