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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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Add LitVar2 link #3737

Closed lynnpais closed 4 months ago

lynnpais commented 11 months ago

Is your feature request related to a problem? Please describe. Add a link to LitVar to improve the ability to search for variants in literature.

Describe the solution you'd like Add a link to Litvar2 at the end of the current options (PubMed, Mastermind, etc.) we have to search the literature for a specific variant. We can use the ClinGen allele identifier to search variants. Here's an example of the Litvar page for the p.T995I variant in NLRP1 - https://www.ncbi.nlm.nih.gov/research/litvar2/docsum?variant=litvar@CA8326971%23rs34733791%23%23&query=CA8326971

Describe alternatives you've considered NA

Additional context Requested by an AnVIL user, but is also useful to other analysts.

hanars commented 11 months ago

We generally do not have the clingen allele identifier for most seqr variants, it would be hard to add it. For MVP lets use hgvs or rsid

hanars commented 10 months ago

actually not possible to link without CAID, blocked on adding it in the pipeline

hanars commented 4 months ago

done. Note this is only available for variants with both RSID and CAID