Liftover MCP Server

This project is an MCP service interface based on the Broad Institute's Liftover tool, providing genome coordinate conversion functions and supporting the conversion of single point, interval, variant, and HGVS formats.

Research and data Developer tools #Genome conversion #Coordinate conversion #Bioinformatics .Python

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update time : 2025-04-29

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What is the Liftover MCP service?

The Liftover MCP service is a programmatic interface that allows users to convert coordinate positions between different genome versions. It is based on the Broad Institute's Liftover tool and can handle the conversion of single positions, intervals, variants, and HGVS notations.

How to use the Liftover MCP service?

You can connect to this service by configuring the MCP client and then send requests containing genome positions and conversion directions. The service will return the converted coordinate positions.

Applicable scenarios

This service is particularly useful when you need to convert gene coordinates between different genome versions (e.g., hg19 to hg38). It is suitable for genome data analysis, variant annotation, and clinical genomics research.

Main features

Single position conversion

Supports the conversion of single genome coordinate positions

Interval conversion

Supports the conversion of genome coordinate intervals (start and end positions)

Variant conversion

Supports the conversion of genome variants containing reference and variant alleles

HGVS notation conversion

Supports the conversion based on transcript ID and HGVS notation

Advantages

Based on the authoritative Liftover tool of the Broad Institute

Supports multiple input formats (single point, interval, variant, HGVS)

The programmatic interface is easy to integrate into the analysis process

Limitations

Currently in the development stage, the API may change

Depends on the network service of the Broad Institute

Does not support batch conversion

How to use

Configure the MCP client

Add the Liftover server to your MCP client configuration

Install dependencies

Ensure that all necessary Python dependencies are installed

Start the server

Run the server program

Usage examples

Convert genome coordinates

Convert the position 141310715 on chromosome 8 of the hg19 version to the hg38 version

Convert HGVS notation

Convert the HGVS variant notation based on hg19 to the hg38 version

Frequently Asked Questions

Does this service support batch conversion?

Which genome versions does it support for conversion?

Do I need to install the local Liftover toolchain?

Related resources

Broad Institute Liftover

Website of the original Liftover tool

FastMCP GitHub repository

Homepage of the FastMCP project

Apache License 2.0

License used by the project

🚀 Lifespan Extension MCP Server

This MCP server provides a programmatic interface for the Liftover tool of the Broad Institute, which can be accessed via liftover.broadinstitute.org.

🚀 Quick Start

Add the MCP Server to Your MCP Server List (Cursor)

{
    "mcpServers": {
      "liftover": {
        "command": "uv",
        "args": ["--directory", "The location where you cloned the repository", "run", "server.py"],
        "env": {}
      }
    }
}

Run MCP Inspector

# Install dependencies
uv sync

# Run MCP Inspector
uv --directory ./ run mcp dev server.py

Run the MCP Server

# Install dependencies
uv sync

# Run the MCP Server
uv run server.py

✨ Features

This MCP server offers a programmatic interface to the Liftover tool from the Broad Institute, enabling users to interact with the tool in a more automated and efficient way.

📦 Installation

Dependencies

uv
mcp[cli]
fastmcp
beautifulsoup4
selenium

Directory Structure

+.
├── server.py            # The main entry file for the FastMCP server
├── liftover_api/        # A Python package containing tool logic and parsers
├── pyproject.toml       # Project metadata and dependencies
└── README.md           # Instructions and documentation

📚 Documentation

MCP Tool Specification

Tool Name

liftover

Input Parameter Examples

Parameter	Type	Required	Description
chr	str	Optional	Chromosome name (e.g., "8" or "chr8")
position	int	Optional	Single position (e.g., 141310715)
start	int	Optional	Start position of the interval (e.g., 141310715)
end	int	Optional	End position of the interval (e.g., 141310720)
ref	str	Optional	Reference allele (e.g., "T")
alt	str	Optional	Alternative allele (e.g., "G")

Version Information

Version: 1.0.0
Release Date: January 1, 2024

📄 License

This software is licensed under the Apache License 2.0. For details, please refer to the LICENSE file.

🔗 Acknowledgments

⚠️ Important Note

🚧 Actively Under Development 🚧

This project is currently in active development. Features and APIs may change without prior notice.