Question about OQL

[Lin Caijin]

Hi. I’m a new user of cbioportal. I used cbioportal to visualize the mutation landscape and I found that mutation type only included inframe indel, missense, truncating (frameshift indel and nonsense), and splicing mutation. How do you deal with nonstop mutation and other rare mutation types (translation start mutation, etc)? Do you just ignore them or classify it as truncating mutation?

Best Regards,

Caijin Lin.

[Ino de Bruijn]

Hi Caijin Lin,

Thanks for reaching out! Nonstop mutations are actually treated as a separate category on many pages. You can find the normalization logic of these different mutation types here:

https://github.com/cBioPortal/cbioportal-frontend/blob/606923486359c008f88954181429ada4d49ea329/packages/cbioportal-frontend-commons/src/lib/getCanonicalMutationType.ts#L56-L110

Hope that helps!

Best wishes,

Ino

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