What problem does it solve?
Researchers needing per-variant GWAS effect sizes (beta, SE, p-value, EAF) for a specific chromosomal window often must download entire multi-gigabyte summary statistics files. This Skill performs a single tabix byte-range fetch against the NHGRI-EBI GWAS Catalog harmonised collection, returning only the variants in the requested region for one GCST study accession.
Core Features & Use Cases
- Tabix range fetch over FTP: Streams only the bytes covering the requested chromosome window from the harmonised
<GCST>.h.tsv.gz file using pysam, avoiding full-file downloads.
- Canonical harmonised output: Maps
hm_* columns to a locuscompare-schema TSV (variant_id, chromosome, position, ref, alt, beta, se, p, eaf) with ALT as the effect allele on GRCh38 forward strand.
- Provenance manifest and report: Writes
manifest.yaml with accession, source URL, fetch timestamp, and variant count, plus a human-readable report.md.
- Use Case: For colocalisation at the SORT1 locus, fetch GCST90269602 (cholesterol in medium VLDL) at chr1:108774968-109774968 and feed the resulting variants.tsv directly into coloc, fine-mapping, or Mendelian randomisation tooling.
Quick Start
Run the bundled demo by asking the agent to fetch the SORT1 cholesterol-VLDL GWAS region with gwas-catalog-region-fetch using --demo and an output directory.
