Hi Everyone, I have been analysing a few cancer samples. I have found some interesting non-coding variants in those samples and wanted to see if they are also present in TCGA data, but could not find any of them replicated in TCGA samples. Does anyone have any information on whether TCGA also reports non-coding variants. If not, what would be the good source to check non-coding variants for different cancers beside COSMIC?
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MAPK
Most of TCGA is exome-only, and the MAF files are specifically restricted to coding variants. For the most part, you'll need to dig into the corresponding VCFs (often unfiltered) or download the bams and call variants yourself.
With DCC credentials, you can find the VCFs at https://tcga-data-secure.nci.nih.gov/tcgafiles/tcga4yeo/tumor/ down paths in the form */gsc/*/*/mutations_protected/
See "To gain access to these data..." https://tcga-data.nci.nih.gov/tcga/tcgaAccessTiers.jsp
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