gwas-lookup

What problem does it solve?

Quickly resolve an rsID to genomic coordinates and collate association, PheWAS, eQTL, and fine-mapping evidence from multiple public genomics APIs so researchers and clinicians can interpret variant-trait relationships without manual API scraping or error-prone aggregation.

Core Features & Use Cases

• Variant resolution: Resolve rsID → chr:pos (GRCh38 + GRCh37), alleles, consequence, and population frequencies using Ensembl with a PortalDev fallback.
• Federated querying: Parallel queries across GWAS Catalog, Open Targets (including credible sets), UKB-TOPMed PheWeb, FinnGen, Biobank Japan (GRCh37), GTEx, and the EBI eQTL Catalogue with rate-limiting and local caching.
• Normalization & reporting: Merge, deduplicate, sort by p-value, flag genome-wide significant hits, and output a reproducible bundle containing a markdown report, CSV tables, figures, raw JSON, and commands for rerunning.
• Use case: Rapidly generate an evidence pack for a candidate variant (e.g., rs3798220) that lists all associated traits, PheWAS hits across biobanks, tissue-specific eQTL effects, and credible set membership for downstream interpretation or manuscript reproducibility.

Quick Start

Use the gwas-lookup skill to look up rs3798220 and generate a full markdown report, CSV tables, figures, and a reproducibility bundle in a specified output directory.