OpenCRAVAT MCP Server

This repository contains an MCP (Model Context Protocol) server that exposes OpenCRAVAT-powered variant annotation as callable tools. It runs as a Cloudflare Worker (via Wrangler) and proxies requests to public OpenCRAVAT services.

What this server provides

It exposes MCP tools that let an MCP client:

• Discover which OpenCRAVAT annotators are being run (a curated default set).

• Inspect annotator output schemas (field names/types/descriptions).

• Annotate variants by:

  • genomic coordinates (chrom/pos/ref/alt). Accepts only GRCh38/hg38 coordinates.

  • dbSNP rsID

  • ClinGen Allele Registry ID (CAid)

  • HGVS (g./c./p.)

• Convert a protein missense notation (e.g., BRAF V600E) into candidate GRCh38 genomic HGVS changes (via SynVar), which you can then pass to HGVS annotation.

Related MCP server: OakVar MCP Server

Connecting

This MCP server is hosted remotely at

https://mcp.opencravat.org/mcp

It can also be run locally.

Claude

To connect to Claude, follow these instructions. Use the URL above, and do not set up auth. No user-specific data is needed for the MCP to work. Remember to enable the MCP for your chat.

ChatGPT

To connect with ChatGPT, you must enable developer mode, then add a custom app:

• Open Settings

• Go to Apps

• In Advanced Settings, use the toggle to turn on “Developer Mode”

• Click Create App

• Use the URL above as the “MCP Server URL”

• Set Authentication to “No Auth”

• Add a name to the MCP App that you’ll easily recognize, such as “OpenCRAVAT”

You will have to add the MCP to a new chat using the + icon in the lower left of the chat box.

Running Locally

Prerequisites:

• Node.js (recent enough for modern TypeScript tooling; Node 18+ recommended)

• npm

Install dependencies:

npm install

Start the dev server (Wrangler):

npm start

By default, your MCP endpoint will be:

http://localhost:8787/mcp

Connect Claude Desktop

To connect to your MCP server from Claude Desktop, follow Anthropic's Quickstart and within Claude Desktop go to Settings > Developer > Edit Config.

Update with this configuration:

{
  "mcpServers": {
    "OpenCRAVAT": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "http://localhost:8787/mcp"
      ]
    }
  }
}

Restart Claude and you should see the tools become available.