Hi all,
I'm a bit lost with TCGA. We are trying to make a global analysis of mutations in genes in cancers categorized per tissue type / cancer type. We thought about utilizing the TCGA data for this, so what I'd basically need is a global maf-file based on the entire TCGA data. However, it appears to me that there is no such file apparently available. I checked the TCGA data portal, but it seems it only lets you query cancer types one by one and then you still have to search for appropriate maf-files. Now I have come across Broad's Firehose portal, where they have a maf-file Dashboard which appears to be regularly updated. They list maf-files from several centers per cancer type, but also sometimes several files from the same center for a single cancer type. Does anyone know if the files listed there should in principal contain all TCGA mutations and I would get a global mutations file by simply combining (and removing duplicates) the maf-files from the Firehose MAF dashboard?
I take it, there is no other data source already containing all TCGA mutations like COSMIC?
Any feedback would be greatly appreciated - thanks!
I'm a bit lost with TCGA. We are trying to make a global analysis of mutations in genes in cancers categorized per tissue type / cancer type. We thought about utilizing the TCGA data for this, so what I'd basically need is a global maf-file based on the entire TCGA data. However, it appears to me that there is no such file apparently available. I checked the TCGA data portal, but it seems it only lets you query cancer types one by one and then you still have to search for appropriate maf-files. Now I have come across Broad's Firehose portal, where they have a maf-file Dashboard which appears to be regularly updated. They list maf-files from several centers per cancer type, but also sometimes several files from the same center for a single cancer type. Does anyone know if the files listed there should in principal contain all TCGA mutations and I would get a global mutations file by simply combining (and removing duplicates) the maf-files from the Firehose MAF dashboard?
I take it, there is no other data source already containing all TCGA mutations like COSMIC?
Any feedback would be greatly appreciated - thanks!
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