GWAS Catalog MCP Server

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About GWAS Catalog MCP Server

No overview available yet

Config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "gwas-catalog-mcp": {
      "command": "uv",
      "args": [
        "sync"
      ]
    }
  }
}

Tools

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Overview

What is GWAS Catalog MCP Server?

This MCP server provides a programmatic interface to the GWAS Catalog REST API, enabling access to GWAS study, variant, trait, and association data. It automatically handles large result sets by offering both in-memory results and file-based storage options.

How to use GWAS Catalog MCP Server?

Install dependencies with uv sync, activate the virtual environment (. .venv/bin/activate), then run the server with uv run server.py. The server exposes a single tool, GWAS_catalog, with multiple endpoints for querying different data types. All endpoints accept common parameters like max_items_in_memory, output_dir, and force_to_file.

Key features of GWAS Catalog MCP Server

Provides programmatic access to GWAS Catalog REST API
Automatic handling of large result sets with file storage
Queries studies, variants, traits, and associations
Supports genome-wide significance filtering (p ≤ 5e-8)
Configurable memory limit and output directory
Removes _links fields from API responses by default

Use cases of GWAS Catalog MCP Server

Retrieve study details and associations for a given study identifier
Search variants in a genomic region and filter by trait
Fetch all associations for a specific variant (with significance flag)
Obtain studies and associations linked to a trait (EFO ID)
Rank top variants associated with a trait

FAQ from GWAS Catalog MCP Server

What happens when results exceed the memory limit?

A subset of results is returned in the items field, is_complete is set to false, and the complete dataset is automatically saved to a file specified in the output_file field.

What dependencies are required to run the server?

The server requires uv, mcp[cli], fastmcp, and requests. Install them with uv sync.

Can I force all results to be written to a file?

Yes. Set the force_to_file parameter to true to always save results to a file regardless of size. Alternatively, use force_no_file to never write to file.

Which endpoints use the GWAS Summary Statistics API instead of the main REST API?

The get_region-trait-associations endpoint and other endpoints marked as "uses GWAS Summary Statistics API" access https://www.ebi.ac.uk/gwas/summary-statistics/api.

Does the server filter results for genome-wide significance?

For endpoints that process p-values (e.g., get_associations_from_variant), only results with is_gwas_significant: true (p ≤ 5e-8) are returned. The metadata includes significant_items count.

Frequently asked questions

What happens when results exceed the memory limit?

A subset of results is returned in the `items` field, `is_complete` is set to `false`, and the complete dataset is automatically saved to a file specified in the `output_file` field.

What dependencies are required to run the server?

The server requires `uv`, `mcp[cli]`, `fastmcp`, and `requests`. Install them with `uv sync`.

Can I force all results to be written to a file?

Yes. Set the `force_to_file` parameter to `true` to always save results to a file regardless of size. Alternatively, use `force_no_file` to never write to file.

Which endpoints use the GWAS Summary Statistics API instead of the main REST API?

The `get_region-trait-associations` endpoint and other endpoints marked as "uses GWAS Summary Statistics API" access `https://www.ebi.ac.uk/gwas/summary-statistics/api`.

Does the server filter results for genome-wide significance?

For endpoints that process p-values (e.g., `get_associations_from_variant`), only results with `is_gwas_significant: true` (p ≤ 5e-8) are returned. The metadata includes `significant_items` count.