Visualization of Exon-Level CNAs in OncoPrint

[Michele Kulesko]

Dear cBioPortal Team,

I am currently working on a dataset that includes not only standard genomic alterations (such as SNVs, CNVs, and structural variants) but also amplifications and deletions at the exon level.
I was wondering whether these exon-level events can be visualized in the main body of the OncoPrint, in a way similar to how SNVs or gene-level CNAs are shown (e.g., red for gains, blue for losses), rather than as annotations in the lower tracks.

Is there currently any supported format or workaround that would allow this?
If not, do you plan to support exon-level resolution or more flexible annotation schemes for OncoPrint in future releases?

I would greatly appreciate any guidance or suggestions you might have on this matter.
Thank you in advance for your time.

Best regards,
Michele

[Nikolaus Schultz]

Dear Michele,

This is a great question. We do not currently have a way to encode these exon level events as copy-number alterations, but there might be a way to encode them as structural variants. Those would then show up as tall purple rectangles in OncoPrints, i.e. as fusions. You can read more about the file format here. 

Niki.

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