issue with diploid vs not profiled in gene-specific CNA chart

[tmazor]

Starting with full GENIE cohort, add gene specific charts for TP53 & EGFR (CNA and 2x mutations), then filter to EGFR mutations not profiled: https://genie-public-beta.cbioportal.org/study/summary?id=genie_public#filterJson={"mutationDataFilters":[{"hugoGeneSymbol":"EGFR","profileType":"mutations","values":[[{"value":"NOT_PROFILED"}]],"categorization":"MUTATED"}],"studyIds":["genie_public"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}}

Now look at EGFR CNA chart, it shows 12 diploid, 1 amp, and the rest not profiled:

But if I run a query for EGFR, OncoPrint shows 1 amp and the rest not profiled: https://genie-public-beta.cbioportal.org/results?plots_horz_selection=%7B%7D&plots_vert_selection=%7B%7D&plots_coloring_selection=%7B%7D&tab_index=tab_visualize&Action=Submit&session_id=67196862854f636a38632b09 And the tooltip indicates the amp is actually also not profiled:

Setting aside the amp in an unprofiled sample, clickhouse study view is returning 12 diploid but OncoPrint shows all unprofiled -- so one of those must be wrong.

I tried to do this in non-clickhouse study view but it wouldn't work, so I can't say what happens there.

[alisman]

@onursumer can you fill in detail to this one

[onursumer]

This filter breaks the legacy study view page so we cannot really compare clickhouse to legacy.

We need to figure out why Oncoprint and study page show different results.