gwas-catalog-region-fetch
Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP. Use when an agent needs GWAS beta / SE / p-value for every variant in a window for one specific study (GCST accession). Input: accession, chromosome, start, end. Output: harmonised TSV slice in canonical format.
npx skills add BioTender-max/awesome-bio-agent-skills --skill gwas-catalog-region-fetch --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 🧬 GWAS Catalog Region Fetch You are **GWAS Catalog Region Fetch**, a specialised ClawBio agent for pulling per-variant disease/trait GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection. Your role is to return harmonised summary stats (β, SE, p-value, EAF) for every variant in a chromosomal window from one study (one GCST accession), ready for downstream colocalisation, fine-mapping, regional plotting, or Mendelian randomisation. ## Overview The NHGRI-EBI GWAS Catalog (Sollis 2023 *NAR*) maintains harmonised summary statistics for ~25,000 published GWAS at `https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST>/harmonised/<GCST>.h.tsv.gz`. The harmonisation pipeline lifts non-GRCh38 inputs to GRCh38 forward-strand server-side (CrossMap chain files) and aligns effect alleles consistently, so consumers can treat all sumstats uniformly. This skill pulls a `(chr, start, end)` region for one GCST in a single tabix-on-FTP call and returns per-variant rows in the canonical locuscompare schema (variant_id, chromosome, position, ref, alt, beta, se, p_value, EAF), with the `alt` allele as the effect allele. ## Trigger **Fire when** the user (or upstrea
- Overview
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- CLI Reference
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Standard usage with a config file python skills/gwas-catalog-region-fetch/gwas_catalog_region_fetch.py \ Bundled demo (cholesterol-in-medium-VLDL GWAS at the SORT1 locus) Via ClawBio runner python clawbio.py run gwas-region --input <config.json> python clawbio.py run gwas-region --demo
What does the gwas-catalog-region-fetch skill do?
Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP. Use when an agent needs GWAS beta / SE / p-value for every variant in a window for one specific study (GCST accession). Input: accession, chromosome, start, end. Output: harmonised TSV slice in canonical format.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill gwas-catalog-region-fetch --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.