Package Exports

variant-linker
variant-linker/src/index.js

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Readme

Variant-Linker

A powerful CLI tool and JavaScript library for genetic variant annotation using Ensembl APIs.

📚 Complete Documentation →

Quick Start

Installation

git clone https://github.com/berntpopp/variant-linker.git
cd variant-linker
npm install
npm link  # Optional: for global CLI access

Basic Usage

# Analyze a single variant
variant-linker --variant "rs6025" --output JSON

# Process VCF file with inheritance analysis
variant-linker --vcf-input sample.vcf --ped family.ped --calculate-inheritance --output VCF

# Batch processing with custom scoring
variant-linker --variants-file variants.txt --scoring_config_path scoring/nephro_variant_score/ --output CSV

Key Features

🔄 Variant Translation - Convert between rsID, HGVS, and VCF formats
📊 VEP Annotations - Comprehensive variant effect predictions
👨‍👩‍👧‍👦 Family Analysis - Inheritance pattern detection from PED files
🗂️ VCF Support - Full VCF input/output with header preservation
⚡ Batch Processing - Efficient handling of large variant datasets
🎯 Custom Scoring - Configurable variant prioritization models
📋 Multiple Formats - JSON, CSV, TSV, and VCF output options

Library Usage

Use Variant-Linker as a library in your Node.js projects:

const { analyzeVariant, variantRecoderPost, vepRegionsAnnotation } = require('variant-linker');

// Analyze a single variant
const result = await analyzeVariant({
  variant: 'rs6025',
  output: 'JSON'
});

// Batch processing
const batchResult = await analyzeVariant({
  variants: ['rs123', 'ENST00000366667:c.803C>T'],
  recoderOptions: { vcf_string: '1' },
  vepOptions: { CADD: '1', hgvs: '1' },
  output: 'JSON'
});

Contributing

Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.

Development Setup

git clone https://github.com/berntpopp/variant-linker.git
cd variant-linker
npm install
npm test
npm run lint

See our Contributing Guide for detailed information.

License

This project is licensed under the MIT License.

Acknowledgements

This tool utilizes the Ensembl Variant Recoder and Variant Effect Predictor APIs, provided by the Ensembl project.