https://github.com/berntpopp/variant-linker
🧬 Powerful CLI tool and JavaScript library for genetic variant annotation using Ensembl APIs. Supports SNVs, CNVs, VCF files, inheritance analysis, batch processing, and genome assembly liftover.
https://github.com/berntpopp/variant-linker
batch-processing bioinformatics cli-tool cnv computational-biology ensembl genetic-variants genetics genome-assembly genomics inheritance-analysis javascript-library liftover medical-genetics nodejs snp variant-annotation variant-calling vcf vep
Last synced: 4 months ago
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🧬 Powerful CLI tool and JavaScript library for genetic variant annotation using Ensembl APIs. Supports SNVs, CNVs, VCF files, inheritance analysis, batch processing, and genome assembly liftover.
- Host: GitHub
- URL: https://github.com/berntpopp/variant-linker
- Owner: berntpopp
- License: mit
- Created: 2024-03-12T18:30:20.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-11-13T17:21:29.000Z (7 months ago)
- Last Synced: 2025-11-13T19:22:15.145Z (7 months ago)
- Topics: batch-processing, bioinformatics, cli-tool, cnv, computational-biology, ensembl, genetic-variants, genetics, genome-assembly, genomics, inheritance-analysis, javascript-library, liftover, medical-genetics, nodejs, snp, variant-annotation, variant-calling, vcf, vep
- Language: JavaScript
- Size: 1.15 MB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Contributing: docs/contributing.md
- License: LICENSE
Awesome Lists containing this project
README
# Variant-Linker
[](https://github.com/berntpopp/variant-linker/actions)
[](https://www.npmjs.com/package/variant-linker)
[](https://opensource.org/licenses/MIT)
A powerful CLI tool and JavaScript library for genetic variant annotation using Ensembl APIs.
## 📚 **[Complete Documentation →](https://berntpopp.github.io/variant-linker/)**
## Quick Start
### Installation
```bash
git clone https://github.com/berntpopp/variant-linker.git
cd variant-linker
npm install
npm link # Optional: for global CLI access
```
#### Windows Installation Issues
If the `variant-linker` command isn't recognized on Windows PowerShell:
**Option 1: Use npx (recommended)**
```powershell
npx variant-linker --help
```
**Option 2: Reinstall globally**
```powershell
npm uninstall -g variant-linker
npm install -g variant-linker
```
### Basic Usage
```bash
# Analyze a single variant
variant-linker --variant "rs6025" --output JSON
# Analyze a copy number variant (CNV)
variant-linker --variant "7:117559600-117559609:DEL" --output JSON
# Process VCF file with inheritance analysis
variant-linker --vcf-input sample.vcf --ped family.ped --calculate-inheritance --output VCF
# Liftover hg19 coordinates to hg38 for annotation
variant-linker --assembly hg19tohg38 --variant "chr17-7578406-C-A" --output JSON
# Batch processing with custom scoring
variant-linker --variants-file variants.txt --scoring_config_path scoring/nephro_variant_score/ --output CSV
# Use HTTP proxy for API requests
variant-linker --variant "rs6025" --proxy http://proxy.company.com:8080 --output JSON
# Use authenticated proxy
variant-linker --variant "rs6025" --proxy http://user:pass@proxy.company.com:8080 --output JSON
```
## Key Features
- 🔄 **Variant Translation** - Convert between rsID, HGVS, VCF, and CNV formats
- 📊 **VEP Annotations** - Comprehensive variant effect predictions including CNV-specific annotations
- 🧬 **Genome Assembly Liftover** - Transparent hg19→hg38 coordinate conversion
- 👨👩👧👦 **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
- 🌊 **Streaming Support** - Memory-efficient stdin processing for pipeline integration
- 🎯 **Custom Scoring** - Configurable variant prioritization models
- 📋 **Multiple Formats** - JSON, CSV, TSV, and VCF output options
- 🎨 **Custom Annotations** - Overlay variants with BED regions, gene lists, and JSON metadata
## Library Usage
Use Variant-Linker as a library in your Node.js projects:
```javascript
const { analyzeVariant, variantRecoderPost, vepRegionsAnnotation } = require('variant-linker');
// Analyze a single variant
const result = await analyzeVariant({
variant: 'rs6025',
output: 'JSON'
});
// Analyze a copy number variant (CNV)
const cnvResult = await analyzeVariant({
variant: '7:117559600-117559609:DEL',
vepOptions: { Phenotypes: '1', numbers: '1' },
output: 'JSON'
});
// Batch processing with mixed variant types
const batchResult = await analyzeVariant({
variants: ['rs123', 'ENST00000366667:c.803C>T', '1:1000-5000:DUP'],
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
```bash
git clone https://github.com/berntpopp/variant-linker.git
cd variant-linker
npm install
npm test
npm run lint
```
See our [Contributing Guide](https://berntpopp.github.io/variant-linker/contributing) for detailed information.
## License
This project is licensed under the [MIT License](LICENSE.md).
## Acknowledgements
This tool utilizes the Ensembl Variant Recoder and Variant Effect Predictor APIs, provided by the Ensembl project.