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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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possible compound, how many are shown? #4855

Closed 4WGH closed 2 weeks ago

4WGH commented 2 weeks ago

The question come up when i analyse a case where this variant in EYS with rank score 24 comes up. I can see several possible intronic compound with lowest rank score 11. => dismiss as no possible compound.

Then I go on with my analys as I need to look at variants down to rank score 10 and I see another variant in EYS, rank score 10.... which acutally is a possible compound ...... And I can see the first variant as dismissed. tHis make me confused.

Do you have a cutoff for the amount of possible compounds shown?

see case F0061527 , the variants are now pinned so you can see them.

dnil commented 2 weeks ago

Hi @4WGH,

I think you are catching it all here, no need for confusion!

The 20 highest scoring compounds are shown for each variant. If a compound variant from the following ranks (21-) exists, and is still scoring high enough to be loaded it would be available on the variantS list. Much as you discover!

Screenshot 2024-09-13 at 16 07 15

And to try to be pedagogical: the highest scoring compound is not "transitive" (or what the term might be here) since the highest scoring variants will be compounds for all variants, whereas the lower scoring ones will show up only in relation to their score. It is less of a pair relation and more of a sorted list on each variant.

dnil commented 2 weeks ago

Im closing this as answered, since there is nothing to fix here, but do get back if you have follow up issues. E.g. one could discuss if the variant at score 10 should have had a slightly higher score (or a lower as it is found in 1.2% of a subpopulation, and >1% in europeans generally) or if the number of highest scoring compounds computed/shown should be 10, 20, 30 or something else...