IGV MCP Server

A Model Context Protocol (MCP) server for controlling [IGV]](https://github.com/igvteam/igv) programmatically through its port interface. This is an experimental project for demonstrating control of IGV-Webapp using MCP from a desktop client, specifically Claude Desktop.

Prerequisites

• Node.js 18 or higher
• IGV running with port command listener enabled (default port: 60151)

Installation

To install the MCP server as a Claude Desktop extension select "Settings" -> "Extensions" -> "Advanced Settings" -> "Install Extension" and select the igvweb.mcpb file from this repository root. Note that currently Claude Desktop runs extensions in a non-sandboxed mode, so it will have full access to your system. Claude will warn you about this.

Development

Clone this repository and install dependencies:

npm install

To run in development mode with the MCP inspector:

npx @modelcontextprotocol/inspector node src/main.js

To build a production version:

npm run build

This will build a bundled igv-mcp.js file in the dist folder, as well as a Claude 'mcpb' package in the root folder.

Usage

Example MCP Client Configuration

The easiest way to configure the client is to add the 'igvweb.mcpb' as an extension to Claude or your client of choice. To manually configure a client add the following to the client configuration json. See the client documentation for more details. The --port must match the port setting in IGV. IGV must be running with port listener enabled. To enable the port listener in IGV, go to View -> Preferences -> Advanced -> and ensure the port option is checked.

{
  "mcpServers": {
    "igv": {
      "command": "node",
      "args": [
        "<oath to>dist/igv-mcp.js",
        "port",
        "60151"
      ]
    }
  }
}

For development, the dist/igv-mcp.js bundle can be replaced withsrc/main.js, but dependencies must be installed.

Running the Server

Normally the server will be started by an MCP client, but you can also start it manually for testing or other purposes

# Default (connects to IGV at 127.0.0.1:60151)
npm start

# Specify custom IGV host/port
node src/main.js --host 127.0.0.1:60151

# Or with a different host
node src/main.js --host 192.168.1.100:60151

Available Tools

The server provides 23 tools for controlling IGV.

Session Management

• new - Reset IGV to a clean state by unloading all data tracks
• saveSession - Save the current IGV session

Genome & Data Loading

• genome - Load a reference genome by ID (e.g., hg38, mm10) or file path
• load - Load data files (BAM, SAM, VCF, etc.)

Navigation & View Control

• goto - Navigate to a genomic locus
• zoomin - Zoom in the view
• zoomout - Zoom out the view

Track Visualization

• collapse - Collapse track to compact representation
• squish - Squish track by reducing row height
• expand - Expand track by increasing row height
• setColor - Set the primary display color for tracks

Region of Interest

• region - Define a region of interest

Alignment Track Organization

• group - Group alignment reads by properties
• sort - Sort reads by various criteria
• viewAsPairs - Toggle paired-end read visualization mode

Sequence Track

• setSequenceStrand - Set which DNA strand to display
• setSequenceShowTranslation - Toggle translation display

Track Overlay

• overlay - Combine multiple wig tracks into a single overlaid track
• separate - Separate an overlaid wig track into component tracks

Snapshots

• snapshot - Capture a snapshot image of the current IGV view
• snapshotDirectory - Set the directory where snapshots will be saved
• maxPanelHeight - Set maximum height for track panels in snapshots