Best way to download hotspot mutations for TCGA samples?
Ruben Drews
Hi,
I am trying to get the mutation information of the cancer hotspot genes for the TCGA cohort. In detail, I want to know which TCGA sample has which mutation in any of the hotspot genes?
Downloading the whole dataset via the “Data Sets” tabs doesn’t work as the column “hotspots” only contains zeros (even for positive hits like BRAF V600E). This is also the case for multiple versions of the data (Pancancer, Firehose, single paper source). The only way I identified to get the data I want is by manually querying the hotspot genes and then download the Mutations file from the Download tab. Is this the best way or is there a more automated (and even a programmatic) way of doing so?
Thank you and best wishes,
Ruben
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Benjamin Gross
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Ruben Drews
Hi Benjamin,
That is good to know. Thank you for pointing me towards Genome Nexus and their APIs!
It looks very close to what I had imagined.
Best,
Ruben
From:
Benjamin Gross <benjami...@gmail.com>
Date: Wednesday, 8 November 2023 at 16:42
To: Ruben Drews <ruben....@gsk.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>, de Bruijn, Ino <debr...@mskcc.org>
Subject: Re: [cbioportal] Best way to download hotspot mutations for TCGA samples?
Hi Ruben, The cBioPortal annotates variants on the fly using our Genome Nexus system (genomenexus. org). I would suggest you write a program to read in a MAF of interest and for each variant make a call to the genome nexus annotation service