Hotspot graph v3 - suggestions and improvements

[davmlaw]

Please add suggestions / ideas here, and leave SACGF/variantgrid_private#277 for critical issues needed to get RUNX1 upgrade complete.

Sarah suggested:

An ultra cool feature (not nec. for now) would be to be able to filter the lollipop by grid e.g. by classification, AF & gnomad MAF. :)

[davmlaw]

Analysis - Add hotspot graph in node genes tab. Either global, or cohort (if in input samples). Editor has gene/transcript autocomplete form (one currently used in cohort hotspot)

Variant classification - graphs/stats page - Add classifications hotspot graph + gene/transcript autocomplete form (one currently used in cohort hotspot)

View gene page - allow full filtering - have stacked analysis nodes (two add widgets at their end of stack - node select up arrow to add above, node select down arrow to add below). Can then build (non-branching) any filter you like while reusing most of the functionality we already have. Need to store analyses - 1 per user/gene to start, can add save features later.

General - classification change symbol. Clinvar too

[davmlaw]

Having ClinVar/internal classification pathogenicity would be good

There's been a bit of demand for having certain types on the top and others on the bottom (eg germline on bottom, somatic on top)

Some other systems bring up a popup when you click on the variant in the graph.

[sksmi]

ProteinPaint, can be embedded and covers everything we'd ever need re. hotspots. Might be a viable alternative to maintaining internally. Not sure of licence options. https://pecan.stjude.org/proteinpaint/TP53 https://docs.google.com/document/d/1JWKq3ScW62GISFGuJvAajXchcRenZ3HAvpaxILeGaw0/edit#

[davmlaw]

Ucsc use this for clinvar which is a variant of lollipops