broadinstitute / genetic-prevalence-estimator

https://genie.broadinstitute.org/
BSD 3-Clause "New" or "Revised" License
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Allow users to add additional variants to list after calculations #95

Closed sambaxter closed 1 year ago

sambaxter commented 2 years ago

It would be helpful to have a way to allow users to add additional variants. Its not uncommon that after we give the list to a group that they find new variants they want us to include. I think this will be a common request so if we can get it into the MVP that would be great. Happy to discuss if adding more would need to only be done through gnomAD IDs

nawatts commented 2 years ago

One option for a minimal version of this feature would be some UI to populate the create custom variant list form with variants from an existing list. Though creating a new list would lose extra information that we want to add in #89, #90, #91. To modify an existing list, we'd need to be able to send the list back through the worker process without losing that info.

We'll need the infrastructure for associating a transcript with a custom variant list from #74 for this. Adding variants to a recommended variant list would change it to a custom list and we would want the consequence annotations to stay the same when it goes back through the worker process.

nawatts commented 2 years ago

If adding variants to a recommended variant list turns it into a custom variant list, we would want to preserve the source column.

nawatts commented 2 years ago

If a variant is re-run through the worker, the version of ClinVar used by the calculator may have changed since the variant list was originally created. This shouldn't affect which variants are included in the list, but may change the clinical significance column. We should explain that this is expected before updating a list.