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 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

oakvar-mcp