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GWAS Catalog MCP Server

@koido

Repository

Basic information

Category

Other

License

Apache-2.0

Transports

stdio

Author

koido

Submitted by

Masaru Koido

About GWAS Catalog MCP Server

No overview available yet

#gwas#bioinformatics

GWAS Catalog MCP Server config

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

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

GWAS Catalog MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

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

Frequently asked questions

1

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.

2

What dependencies are required to run the server?

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

3

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.

4

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`.

5

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.

Comments

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