Categorical CNVs

[DanielPuthawala]

Let's discuss CNVs!

Currently in the test set we only have this EGFR copy number variant on the docket. Feel free to expand.

From the discussion earlier today there were unresolved issues on (among other things)

• absolute quantitative values (as in copy count)
• relative quantitative value (copy change)
• categorical changes (loss / gain / high-level gain...)
• quantitative measure as a weighted average of noisy samples (different purities of samples, cells from different clonal expansions, etc)
• vrs: location vs vrs: definingContext

What are your thoughts on these, and what we need to cover?

[DanielPuthawala]

I think we've progressed beyond the scope of this discussion in the main constraint model discussion thread.