Download mutation data

[Mccann, Patrick]

To Whom It May Concern,

We are trying to download mutation data for a selected patient cohort, but we’re having trouble exporting the full set of sample-level mutational profiles, including mutation types (e.g., missense, nonsense) and OncoKB annotations, which are typically available on individual sample pages.

Could you please advise on how to access or export this information for the entire cohort? Thank you!

Best Regards,

Pat McCann

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[Schultz, Nikolaus]

Hi Pat,

There is currently no way to download the full mutation data directly through cBioPortal, but you can download the full files for individual studies via the DataHub for the public cBioPortal. Note that these files are not contain the OncoKB annotations (we update OncoKB annotations in real time in cBioPortal), so you would have to annotate them using the OncoKB annotator tool. 

If this question is about access to a private, MSK-internal data set, please email me directly and we can point you in the right direction.

Niki.

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