Hi, I've been sifting through TCGA vcfs and though I've seen references to germline mutation calls in some pages, I can't actually find any (even among controlled data). The mutect and varscan vcfs seem to only include somatic. Are there actually any vcfs that contain germline variants? Thanks.
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Liberty Mutual customizes your car insurance so you only pay for what you need .. but ya unfortunately the GDC Data Portal doesn't customize your VCFs so you only download the variants you need.
It’s a bit tricky. While TCGA possesses germline variant data, it is not distributed as a standard, individual-level VCF product through their primary exploration tools. The standard pipelines (using callers like MuTect2, VarScan2, etc.) are strictly designed for somatic mutation calls. If I'm not mistaken, the PanCanAtlas AWG page is still one of the best places to get actual germline calls, though i havent looked in some time and there might be better source ...
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