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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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"Classify-link" on the Clinical Structural variants-variant page #4596

Open SofieCMD opened 6 months ago

SofieCMD commented 6 months ago

Variant page in the Clinical Structural variants module: Is it possible to link to a fillable CNV classification template saved in Scout after filling in, as for the ACMG calssification in the SNVs/indel module?

Maria Bååth (Lund) has created attached template from the on-line tools (https://cnvcalc.clinicalgenome.org/cnvcalc/cnv-loss and https://cnvcalc.clinicalgenome.org/cnvcalc/cnv-gain)

_Labnr XXXX - Bedömningsmall för kopietalsvariant (Riggs et al., 2020).xlsx

northwestwitch commented 6 months ago

Nice suggestion! I guess It would be appreciated by clinicians in Stockholm too. It's not a super easy feature to implement so perhaps good to tackle during periods when our workload is less intense or for a student/intern to take on.

dnil commented 6 months ago

It would add good symmetry to the SNV ones, and the classification seems solid but a little arbitrary (sliding scales allowing user knowledge feedback, but also user bias). Since it is not (yet?) in use in Solna, another suggestion would also be to nudge your local devs with it - that way we each bring what we do well into the framework!

Note that we did add a link to the online tools via https://github.com/Clinical-Genomics/scout/issues/4476, so for now you could use it and note the criteria ticked and fractional scores assigned in a (possibly global) comment.😊 Obviously it will be more useful with actual classifications stored on db eventually.