liftover-mcp
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This MCP server provides a programmatic interface to the Broad Institute's Liftover tool.
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 file for details.
