This MCP server provides a programmatic interface to the Broad Institute's Liftover tool, which is available at liftover.broadinstitute.org.
🚧 Under Active Development 🚧
This project is currently under active development. Features and APIs may change without notice.
uv- mcp[cli]
- fastmcp
- beautifulsoup4
- selenium
+.
├── 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
{
"mcpServers": {
"liftover": {
"command": "uv",
"args": ["--directory", "where you cloned the repo", "run", "server.py"],
"env": {}
}
}
}# Install dependencies
uv sync
# Run MCP Inspector
uv --directory ./ run mcp dev server.py# Install dependencies
uv sync
# Run the MCP server
uv run server.py- liftover
| 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
- 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
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.
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
This MCP server itself is licensed under the Apache License 2.0 - see the LICENSE file for details.