OakVar MCP Server

A Model Context Protocol (MCP) server that exposes OakVar's genomic variant analysis capabilities to AI assistants.

Supported MCP Clients: Claude Desktop, ChatGPT Desktop, and other MCP-compatible clients.

Quick Start

# 1. Install OakVar and the MCP server
pip install oakvar oakvar-mcp

# 2. Setup OakVar (first time only)
ov system setup

# 3. Configure your MCP client (see SETUP.md)

📖 Full setup instructions: See SETUP.md

What is This?

This MCP server lets you control OakVar through AI assistants like Claude or ChatGPT. Instead of running command-line tools, you can simply ask:

• "What OakVar modules are installed?"
• "Install the ClinVar annotator"
• "Run OakVar on my VCF file with gnomAD annotation"
• "Show me pathogenic variants from the results"

Features

Category	Capabilities
Pipeline	Run annotations, generate reports (VCF, Excel, CSV)
Modules	Install, update, list, search 200+ annotator modules
Data	Query result databases, filter variants, export data
Development	Create module templates, pack for distribution

Architecture

┌─────────────────┐     MCP Protocol     ┌──────────────────┐
│   Claude /      │◄────────────────────►│  OakVar MCP      │
│   ChatGPT       │    (stdin/stdout)    │     Server       │
└─────────────────┘                      └────────┬─────────┘
                                                  │
                                                  │ Python API
                                                  ▼
                                         ┌──────────────────┐
                                         │     OakVar       │
                                         │ Variant Analysis │
                                         └──────────────────┘

Installation

Note: OakVar and this MCP server must be installed in the same Python environment. If you use a virtual environment, configure your MCP client to use the full path to that environment's oakvar-mcp executable.

<!--

From PyPI

pip install oakvar-mcp

-->

From Source

git clone https://github.com/zaroganos/oakvar-mcp.git
cd oakvar-mcp
pip install -e .

Configuration

Claude Desktop

Add to claude_desktop_config.json:

{
  "mcpServers": {
    "oakvar": {
      "command": "oakvar-mcp"
    }
  }
}

ChatGPT Desktop

Add to chatgpt_mcp_config.json:

{
  "mcpServers": {
    "oakvar": {
      "command": "oakvar-mcp"
    }
  }
}

📖 Config file locations and troubleshooting: See SETUP.md

Available Tools (19)

Tool	Description
oakvar_version	Get OakVar version
oakvar_system_check	Verify installation
oakvar_system_setup	Configure OakVar
oakvar_modules_dir	Get/set modules directory
oakvar_module_list	List modules
oakvar_module_info	Get module details
oakvar_module_install	Install modules
oakvar_module_uninstall	Remove modules
oakvar_module_update	Update modules
oakvar_run	Run annotation pipeline
oakvar_report	Generate reports
oakvar_sqliteinfo	Get database info
oakvar_filtersqlite	Filter databases
oakvar_query	Execute SQL queries
oakvar_new_module	Create module templates
oakvar_new_exampleinput	Create test inputs
oakvar_module_pack	Pack for distribution
oakvar_store_fetch	Refresh store cache
oakvar_store_register	Register modules

Development

# Clone and install in dev mode
git clone https://github.com/zaroganos/oakvar-mcp.git
cd oakvar-mcp
pip install -e ".[dev]"

# Run tests
pytest tests/ -v

Project Structure

oakvar-mcp/
├── oakvar_mcp/
│   ├── __init__.py
│   ├── __main__.py
│   └── server.py
├── tests/
│   └── test_server.py
├── pyproject.toml
├── README.md
├── SETUP.md
├── claude_desktop_config.example.json
└── chatgpt_mcp_config.example.json

License

MIT License

Links

• OakVar Documentation
• OakVar GitHub
• Model Context Protocol