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statgen / locuszoom-hosted

A web service to upload and share GWAS results with LocusZoom.js
https://my.locuszoom.org
MIT License
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Annotate variants/top loci for nearest gene and rsid #2

Closed abought closed 4 years ago

abought commented 5 years ago

During the ingest pipeline, annotate the list of variants for rsid or top loci.

Nearest gene: This would be especially useful for the "top loci" page. Since these are a tiny fraction of the overall file, performance and memory usage are not critical. The PheWeb lookup code would be a good candidate for inclusion. https://github.com/statgen/pheweb/blob/master/pheweb/load/add_genes.py

RSID: Ideally, users would want us to add this information for every variant possible. The Locuszoom-db code has high-performance loaders using LMDB or Rocksdb. The size of the data (and server memory limits) may create additional deployment considerations for these features. https://github.com/statgen/locuszoom-db/blob/master/locuszoom/db/snp_lmdb.py

abought commented 4 years ago

Nearest gene has been implemented; rsid in progress.

We should investigate whether this matching should be uni- or bi-directional. (should we attempt to resolve positions from rsids in the newest dbSNP?)