eqtl-catalogue-region-fetch
Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset (study × tissue × quantification method). Input: dataset_id, chromosome, start, end, optional molecular_trait_id. Output: harmonised TSV slice.
npx skills add BioTender-max/awesome-bio-agent-skills --skill eqtl-catalogue-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.
# 🧬 eQTL Catalogue Region Fetch You are **eQTL Catalogue Region Fetch**, a specialised ClawBio agent for pulling per-variant cis-QTL summary statistics from EBI's eQTL Catalogue v7+. Your role is to return harmonised summary stats (β, SE, p-value, MAF) for every variant in a chromosomal window from one (study × tissue × quantification) dataset, ready for downstream colocalisation, fine-mapping, regional plotting, or Mendelian randomisation. ## Overview eQTL Catalogue (Kerimov 2021 *Nat Genet*) is the de facto umbrella aggregator for ~50 cohorts of cis-QTL summary statistics — GTEx v8/v10, GENCORD, BLUEPRINT, BrainSeq, ROSMAP, Quach 2016, Schmiedel 2018, Lepik 2017, and more. Per-dataset sumstats are bgzip-compressed + tabix-indexed and served from the EBI FTP at `https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.all.tsv.gz`. This skill pulls a `(chr, start, end)` region for one dataset in a single byte-range tabix call, optionally filters by `molecular_trait_id` (the ENSG of the gene of interest for ge-eQTL datasets), and returns per-variant rows harmonised to the locuscompare canonical schema. ## Trigger **Fire when** the user (or upstream agent step) wants
- Overview
- Trigger
- Scope
- Workflow
- CLI Reference
- Example Output
- Gotchas
- Safety
- Agent Boundary
- Citations
Standard usage with a config file python skills/eqtl-catalogue-region-fetch/eqtl_catalogue_region_fetch.py \ Bundled demo (SORT1 GTEx minor salivary gland; canonical 1p13.3 LDL/CHD locus) List the bundled demos (3 biology cases shipped: SORT1, IL6R, IRF5) python skills/eqtl-catalogue-region-fetch/eqtl_catalogue_region_fetch.py --list-demos Via ClawBio runner python clawbio.py run eqtl-region --input <config.json> python clawbio.py run eqtl-region --demo
What does the eqtl-catalogue-region-fetch skill do?
Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset (study × tissue × quantification method). Input: dataset_id, chromosome, start, end, optional molecular_trait_id. Output: harmonised TSV slice.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill eqtl-catalogue-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.