search

populationgenomics / production-pipelines

Genomics workflows for CPG using Hail Batch
MIT License
6 stars 1 forks source link

SeqrSV - variant DB links (gnomAD, Iranome) links incorrect #501

Closed MattWellie closed 11 months ago

MattWellie commented 11 months ago

Hyperlink to SV in gnomAD/other DBs not appearing correctly. gnomAD doesn't appear at all, and other links are busted.

Screenshot 2023-11-03 at 11 33 02 am

Links being generated in the form https://databrowser.researchallofus.org/genomic-variants/1-987395-null-null where null-null should be populating with ref-alt (here)

The gnomAD links for SVs aren't displaying at all, so this shouldShow condition is False. That suggests that svType is populating, but either variant.svType is not, or the has37Coords test is failing (or both)

Is this where the liftedOverPos is coming from? If so, it should be populated, as the MT & EsIndex have rg37_locus populated

MattWellie commented 11 months ago

I am a silly dumb dumb - likely solved by a correction to the svType attribute. Closing for now