How do I obtain germline mutation for TCGA samples?

Question

[Les Ander]

Hello, I have obtained approval from the TCGA to obtain control data. I can log in and see the search page at the data portal (https://gdc-portal.nci.nih.gov/). However, I am not able to figure out how to find the germline mutation data for each of the cancer types. Any help would be much appreciated. Les

Answer 1

[alserg]

The only way that worked for me was to go to GDC Legacy Archive and download protected vcfs from there. In the new version I couldn't find germline mutation calls anywhere, even in protected MAFs and VCFs.

[komal.rathi]

If the files are protected, do you need to request access to them?

[alserg]

Yes. You still need a key for the protected data.

Answer 2

[mforde84]

when you look at the available vcf files, there will some that are protected. those will include both somatic and germline calls. so you can intersect with the unprotect somatic calls to get what you want. alternatively you could always use the bam files to generate calls using any number of germline variant callers, haplotype caller, pileup, etc. the later is probably more rigorous.

Answer 3

[passage543]

hello

I have the same question about how can I get germline mutation data form TCGA legacy archive ? I have been tried using GDC token ,but the maf and vcf which I download can not find germline mutation .

THANKS for any help