broadinstitute / seqr-loading-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
MIT License
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add annotation clinical_significances for clinvar submission #760

Closed jklugherz closed 4 months ago

hanars commented 4 months ago

I don't think this does what we want. The update based on the seqr ticket was to show the clinical significance associated with each submitter. This is aggregating the submitters and the clinical significances independently so the relationship will be lost.

Lynn said on that ticket that we should only add this if it would be easy, and I said there that since this required upstream pipeline changes its not easy and we should not do it. The fact that there seems to be a bunch of complexity and iteration needed for this in the pipeline makes me feel that even more. I do not think we want to add this functionality now at all, and should leave this out of the MVP.

bpblanken commented 4 months ago

FWIW I think Julia was able to do this before the comment about not proceeding:

Screenshot 2024-04-11 at 12 14 21 PM Screenshot 2024-04-11 at 12 14 41 PM

let's discuss in standup!