Liftover MCP server

Overview

This MCP server provides a programmatic interface to the Broad Institute's Liftover tool, which is available at liftover.broadinstitute.org.

Status

🚧 Under Active Development 🚧

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

Dependencies

• uv
• mcp[cli]
• fastmcp
• beautifulsoup4
• selenium

Directory structure

+.
├── server.py            # Main FastMCP server entrypoint
├── liftover_api/        # Python package with tool logic and parsers
├── pyproject.toml       # Project metadata and dependencies
└── README.md           # Usage and documentation

Setup and Running

Add the MCP server to your MCP server list (Cursor)

{
    "mcpServers": {
      "liftover": {
        "command": "uv",
        "args": ["--directory", "where you cloned the repo", "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

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	Interval start position (e.g., 141310715)
end	int	Optional	Interval end position (e.g., 141310720)
ref	str	Optional	Reference allele (e.g., "T")
alt	str	Optional	Alternate allele (e.g., "G")
transcript	str	Optional	Transcript ID (e.g., "NM_001089.3")
c_dot	str	Optional	c. notation (e.g., "c.875A>T")
p_dot	str	Optional	p. notation (e.g., "p.Glu292Val")
from_genome	str	Required	Source genome (e.g., "hg19")
to_genome	str	Required	Target genome (e.g., "hg38")

• Specify only the required parameters for each input format

Input examples

• chr=8, position=141310715, from_genome=hg19, to_genome=hg38
• chr=8, start=141310715, end=141310720, from_genome=hg19, to_genome=hg38
• chr=8, position=141310715, ref=T, alt=G, from_genome=hg19, to_genome=hg38
• transcript=NM_001089.3, c_dot=c.875A>T, p_dot=p.Glu292Val, from_genome=hg19, to_genome=hg38

Please follow the liftover.broadinstitute.org

Credits

This tool relies on the Broad Institute's Liftover web service. All coordinate conversion functionality is provided by their service.

Please cite and credit the Broad Institute when using this tool in your work.

Visit liftover.broadinstitute.org for more information about the original service.

Release Notes

v0.1.0-alpha (2025-04-22)

Initial alpha release with basic functionality:

• ✨ Basic liftover functionality implementation
• 🎯 Support for single position conversion
• 🎯 Support for interval conversion
• 🎯 Support for variant conversion
• 🎯 Support for HGVS notation conversion
• 📚 Basic documentation and usage examples

License

This MCP server itself is licensed under the Apache License 2.0 - see the LICENSE file for details.

Acknowledgements

• liftover.broadinstitute.org
• FastMCP