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eqtl-catalogue-region-fetch

Fetch cis-eQTL summary statistics for a genomic region from EBI eQTL Catalogue via tabix.

1.1k|257|Updated Feb 25, 2026
Search Tags:#bioinformatics#genomics#summary statistics#eQTL#eqtl-catalogue#colocalisation#tabix
One-click install
npx skills add https://github.com/ClawBio/ClawBio --skill eqtl-catalogue-region-fetch
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: eqtl-catalogue-region-fetch
Source: https://github.com/ClawBio/ClawBio/tree/main/skills/eqtl-catalogue-region-fetch
Command: npx skills add https://github.com/ClawBio/ClawBio --skill eqtl-catalogue-region-fetch

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pysam, pandas, requests.

What problem does it solve?

Researchers doing colocalisation, fine-mapping, or Mendelian randomisation need per-variant eQTL effect sizes (beta, SE, p-value) for a genomic window, but the eQTL Catalogue REST API silently truncates regional queries and ignores position filters, making reliable regional retrieval difficult.

Core Features & Use Cases

  • Tabix-on-FTP region fetch: Pulls a full strand-aware cis-window slice from the EBI FTP .all.tsv.gz / .cc.tsv.gz files in a single byte-range request, avoiding the broken REST associations endpoint.
  • Harmonised output: Emits a locuscompare-schema TSV (variant_id, chromosome, position, ref, alt, beta, se, p, maf) in GRCh38 ALT-effect convention, plus a provenance manifest and human-readable report.
  • Trait filtering and caching: Filters by molecular_trait_id or gene_id (required for ge datasets bundling all genes), auto-resolves study IDs via metadata REST, and caches fetched slices locally.
  • Use Case: Given the SORT1 locus at 1p13.3, fetch all GTEx minor salivary gland ge-eQTL summary statistics for a 1 Mb window and feed the TSV directly into a colocalisation analysis against a GWAS of LDL cholesterol.

Quick Start

Ask the agent to fetch the eQTL summary statistics for SORT1 (ENSG00000134243) in GTEx minor salivary gland over chromosome 1:108774968-109774968 using the bundled demo.

Frequently Asked Questions about eqtl-catalogue-region-fetch

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I fetch eQTL summary statistics for a genomic region from eQTL Catalogue?▼

Provide a dataset_id (e.g. QTD000276), chromosome, and 1-based GRCh38 start and end coordinates. The skill performs a single tabix byte-range fetch against the EBI FTP per-variant file and returns a harmonised TSV with beta, SE, p-value, and MAF per variant.

Why use tabix on FTP instead of the eQTL Catalogue REST API?▼

The v2 REST associations endpoint silently truncates regional fetches to one side of the TSS and ignores pos_min/pos_max parameters. The tabix-indexed FTP files serve the full strand-aware ±1 Mb cis-window correctly, so they are the reliable fetch path.

Do I need to pass a molecular_trait_id when querying eQTL Catalogue data?▼

For ge (gene expression) datasets, yes: the harmonised file bundles every gene's variants together, so without an Ensembl gene ID filter you get all genes' rows in the window. Other quantification methods like tx, txrev, exon, and leafcutter have similar bundling behavior.

Can this skill fetch pQTL, trans-eQTL, or fine-mapping credible sets?▼

No. It only fetches cis-eQTL nominal summary statistics from eQTL Catalogue. For pQTL use a UKB-PPP fetcher, for trans-eQTL use resources like eQTLGen, and for SuSiE credible sets with PIPs use a dedicated fine-mapping skill.

What dependencies are required to run the eQTL region fetch?▼

You need Python 3.10 or later with pysam (for tabix range queries), pandas, and requests installed, plus network access to the EBI FTP and metadata REST endpoints. A conda environment.yml is provided for setup.

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