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Find mutation rates for a set of genes

Hi,

I am trying to find out how I can find the mutation frequency among various cancers for each gene in a set of around 700 genes that I'm interested in. On cBioPortal it is only possible to query 100 genes at a time and I haven't managed to download their data for my set of genes, any suggestions for how to do this?

Frida

cancer mutations cbioportal tcga
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updated by poisonAlien poisonAlien • written by frida.danielsson • frida.danielsson

1 answer

you would be better off with downloading MAF files for all 33 TCGA cohorts and estimate yourself.

You can use firehose to download all.

firehose_get -tasks mutsig analyses latest

This would download all MutSig results including stable maf file that broad uses for their downstream analyses.

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written by poisonAlien poisonAlien

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