Variant-Linker is a command-line interface (CLI) tool designed to facilitate the retrieval of genetic variant annotations. It integrates with Ensembl's Variant Recoder and Variant Effect Predictor (VEP) REST APIs to provide a streamlined process for obtaining detailed annotations for a given genetic variant.
Before installing Variant-Linker, ensure you have Node.js and npm (Node Package Manager) installed on your system.
To set up Variant-Linker, follow these steps:
Clone the repository:
git clone https://github.com/your-github-username/variant-linker.git
cd variant-linker
Install dependencies:
npm install
Link the package globally (optional but recommended):
npm link
After installation, you can run Variant-Linker using the following command:
variant-linker --variant <variant_input> --output <output_format> [--debug]
--config
, -c
: Path to the configuration file.--variant
, -v
: Specify the genetic variant to be analyzed. This can be provided via command line or configuration file.--output
, -o
: Define the desired output format (e.g., JSON, CSV). Default is JSON.--save
, -s
: Filename to save the results. If not specified, results will be printed to the console.--debug
, -d
: Enable debug mode for detailed logging. This is optional and is not enabled by default.--vep_params
, -vp
: Optional parameters for VEP annotation in key=value format, separated by commas (default: "CADD=1").--recoder_params
, -rp
: Optional parameters for Variant Recoder in key=value format, separated by commas (default: "vcf_string=1").--scoring_config_path
, -scp
: Path to the scoring configuration directory.Variant-Linker can accept a JSON configuration file to specify parameters. Command-line parameters will override configuration file parameters if both are provided.
example_input.json
):{
"variant": "ENST00000366667:c.803C>T",
"output": "JSON",
"save": "output/example_output.json",
"debug": 3,
"scoring_config_path": "scoring/meta_score/"
}
Variant-Linker can detect and process variants provided in VCF format. When a VCF formatted variant is detected, the tool:
1-65568-A-C
1:65568-65568:1
C
Using command-line parameters:
variant-linker --variant 'ENST00000366667:c.803C>T' --output JSON
Using a configuration file:
variant-linker --config example_input.json
Contributions to Variant-Linker are welcome. Please feel free to fork the repository, make your changes, and submit a pull request.
This project is licensed under the MIT License.
This tool utilizes the Ensembl Variant Recoder and Variant Effect Predictor APIs, provided by the Ensembl project.