Find mutation rates for a set of genes

Question

[frida.danielsson]

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

Answer 1

[poisonAlien]

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.

[frida.danielsson]

Thanks! I will look into that.