Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Inheritance models on variantS page not correctly displayed #4882

Open dnil opened 2 hours ago

dnil commented 2 hours ago

On the gene hover on the variantS page, not all (OMIM) inheritance models are always shown. They are visible on the variant page and gene page, but quick operators scan the variantS page for ez dismisses like missing compounds, and may rely on the inheritance pattern. A quick sample had it ok for several genes with more than one disease, but we have one confirmed report with COL6A3 (https://scout.scilifelab.se/cust002/F0060227/a3d33632dae34dae1b3ff41743e7853d)...

Screenshot 2024-09-20 at 09 54 05

Screenshot 2024-09-20 at 09 54 23

Screenshot 2024-09-20 at 09 54 50

Maybe the get-rid-of ORPHA logic failing?

dnil commented 2 hours ago

Good with the delete, did you report it as well?

northwestwitch commented 2 hours ago

Good with the delete, did you report it as well?

No, how do I do it?

northwestwitch commented 2 hours ago

Ah someone else probably did, that user is gone

dnil commented 2 hours ago

Anyway. It looks like the inheritance is already botched on the variant. 😞

Screenshot 2024-09-20 at 10 07 21
dnil commented 2 hours ago

Good with the delete, did you report it as well?

No, how do I do it?

There is like an option on the dropdown to "report content". 😊

dnil commented 1 hour ago

Soo, it was ok in Nov 2023...

Screenshot 2024-09-20 at 10 38 00

And in Feb 2024...but not in April 2024. Maybe that is narrow enough. Lets see.

dnil commented 1 hour ago

It has to be this - https://github.com/Clinical-Genomics/scout/pull/4443. It is actively hiding inheritance patterns. Only likely a bit too many...

dnil commented 1 hour ago

Nope, it surprisingly looks ok. Also it was released on 4.78 (deployed on hasta 28/2) and slightly later cases are ok - e.g. in March 2024 (2024-03-07). https://scout.scilifelab.se/cust002/F0059087

dnil commented 1 hour ago

Sooo, 4.79 perhaps? Yes, the error is present on 2024-03-19.