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broadinstitute / seqr

web-based analysis tool for rare disease genomics
GNU Affero General Public License v3.0
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Refresh saved searches #4450

Closed lynnpais closed 2 weeks ago

lynnpais commented 3 weeks ago

Is your feature request related to a problem? Please describe. As discussed, remnants of prior annotations exist in our saved searches. As a result, variants are returned even if the annotation is not selected.

Here's an example of a de novo/dominant search returning variants (SVs, missense, synonymous) that were not selected. Note: I did modify the search to only include nonsense variants. Also set the inheritance to ? for the parents so that we have more variants as examples.

Describe the solution you'd like Update/refresh our four saved searches: de novo/dominant restrictive and permissive + recessive restrictive and permissive.

Describe alternatives you've considered NA

Additional context Discussed earlier this week.

hanars commented 3 weeks ago

In the body of the ticket you say "heres an example" but theres no link - I think you forgot to add it

lynnpais commented 3 weeks ago

Whoops! Here's the link to a dominant permissive search - https://seqr.broadinstitute.org/variant_search/results/f940e1c926462b46b992a144fd171c02?page=1&sort=in_omim

It was modified as described above.

hanars commented 2 weeks ago

Searches have been updated. The particular search you linked is still saved with the old values, but going forward if you edit the standard searches they will not have any "secret" annotations in them anymore, and unchecking the structural consequences, for example, will mean no structural variants are included