Hello everyone,

I am interested in analyzing some data from TCGA, specifically the LAML project. From there I managed to download the HTSeq counts for the whole cohort, however I would like to map each sample to specific mutations for given set of genes in order to perform DE analysis between pools of samples with the same gene mutated. 

I am struggling with this second part. I found a R package named RTCGAToolbox in which you can download the expression data and the Mutation data among others. Instead, what I am getting are the mutations present in the cohort rather than a table to map samples with their mutations. Is there any possibility to download this kind of metadata, or I have to manually check from MAF files for each sample? If I have to, how should I do it?

Thanks in advance to everyone,

Esteve

P.S: Checked before writing this post if there was any similar one, but I didn't find any. Apologies if it is a repeated question.
I did a lot of the analysis for the TCGA AML paper. The simplest way to pull mutations is to go to the [paper's supplemental site](https://tcga-data.nci.nih.gov/docs/publications/aml_2012/) and pull Supplemental Table 6.  Note that the variants are all on build 36, so liftover may be in order if you're working from a newer reference genome build.



