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.

Connecting

This MCP server is hosted remotely at

https://mcp.opencravat.org/sse

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/sse

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/sse"
      ]
    }
  }
}

Restart Claude and you should see the tools become available.