eqtl-catalogue-region-fetch

name	eqtl-catalogue-region-fetch
description	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.
license	MIT
metadata	{"skill-author":"Aviv Madar","version":"0.1.0","domain":"bioinformatics","tags":["eqtl","eqtl-catalogue","region-fetch","tabix","summary-statistics","cis-eqtl"],"inputs":[{"name":"dataset_id","type":"string","description":"eQTL Catalogue dataset identifier (e.g. QTD000276 for GTEx minor salivary gland ge-eQTL).","required":true},{"name":"chromosome","type":"string","description":"Chromosome name without `chr` prefix (1, 2, ..., X, Y, MT).","required":true},{"name":"start_bp","type":"integer","description":"Region start, 1-based GRCh38.","required":true},{"name":"end_bp","type":"integer","description":"Region end, 1-based GRCh38 (inclusive).","required":true},{"name":"molecular_trait_id","type":"string","description":"Optional ENSG (versioned or bare) to filter to one gene; required for ge-eQTL datasets where one TSV bundles multiple traits.","required":false}],"outputs":[{"name":"variants","type":"list","description":"Per-variant rows with variant_id, chromosome, position, ref, alt, beta, se, p_value, maf, molecular_trait_id, dataset_id."},{"name":"release","type":"object","description":"EQTLCatalogueRelease with study_label, tissue_label, condition_label, sample_group, quant_method, dataset_release, fetched_at_utc."}],"dependencies":["python>=3.10","pysam>=0.22","pandas>=2.0","requests>=2.28"],"demo_data":["examples/input.json"],"endpoints":["https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/","https://www.ebi.ac.uk/eqtl/api/v3/"],"openclaw":{"requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"always":false,"emoji":"🧬","homepage":"https://github.com/ClawBio/ClawBio","os":["darwin","linux"],"install":"pip install pysam pandas requests\n","trigger_keywords":["eqtl region fetch","eqtl catalogue tabix","eqtl sumstats slice","cis-eqtl region pull","GTEx eqtl region"]}}

🧬 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:

• A regional slice of cis-eQTL summary statistics (β, SE, p-value) for variants around a gene's TSS, from one (study × tissue × quant_method) in eQTL Catalogue.
• Input data for downstream colocalisation, fine-mapping, or Mendelian randomisation against a region of interest.
• Provenance-rich, harmonised eQTL summary stats with allele orientation preserved (ALT-effect β).

Do NOT fire when the user wants:

• A point lookup of one variant in one tissue: query the GTEx Portal REST API (https://gtexportal.org/api/v2/) directly for single-variant queries.
• All eQTLs for a gene across all tissues: this skill returns one (study × tissue × quant_method) at a time. Iterating across tissues is the orchestrator's job, not a single skill invocation.
• pQTL data: eQTL Catalogue does not host pQTL summary statistics. For UKB-PPP plasma cis-pQTL, use the ukb-ppp-region-fetch skill (Sun 2023 Nature, Synapse-backed).
• trans-eQTL data: eQTL Catalogue's cis-window is ±1 Mb of TSS; trans-eQTL signals are at distant variants and require a different upstream (e.g., eQTLGen for blood trans).
• Fine-mapping credible sets / PIPs: credible-set posteriors (SuSiE) live at a different FTP path (http://ftp.ebi.ac.uk/pub/databases/spot/eQTL/susie/) and require a separate skill. For SuSiE / SuSiE-inf / ABF fine-mapping with PIPs and credible sets, use the sibling skill already on ClawBio main. The nominal-pass files this skill fetches do NOT include posterior inclusion probabilities.