How do I get germline mutation data from TCGA ?

Question

[passage543]

Hello

I can not find germline mutation data from TCGA legacy archive. I have been looking from VCF MAF file even controlled data but still can't find. thanks for any help

Answer 1

[Kevin Blighe]

Those are only available in the controlled data, but they should be there in the GDC Legacy, possibly as aligned BAMs. You will be able to distinguish tumour from germline samples based on the TCGA barcode. See here for further details: how to find sample type information from TCGA?

See also Understanding TCGA Barcodes

If you download the open data in MAF format, then these are somatic mutations and will already have been filtered for germline variants, as much as I'm aware. There will additionally be a column in the MAF file called 'panel_of_normals', which are variants called in an unrelated panel of healthy controls. You can filter out variants that are called as somatic that are also found in this panel of normals, too.

Kevin