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Introduction

Welcome to Variant-Linker, a powerful command-line interface (CLI) tool and JavaScript library for genetic variant annotation.

What is Variant-Linker?​

Variant-Linker is designed to facilitate the retrieval of genetic variant annotations by integrating with Ensembl's Variant Recoder and Variant Effect Predictor (VEP) REST APIs. It provides a streamlined process for obtaining detailed annotations for genetic variants.

In addition to its CLI capabilities, Variant-Linker features a modular architecture that allows its core functionalities to be easily imported and used as an API within other Node.js projects.

Key Features​

  • 🔄 Variant Translation: Converts genetic variant inputs into various formats to all possible variant IDs and HGVS notations
  • 📊 VEP Annotations: Retrieves detailed variant annotations from the VEP API
  • 🔍 Filtering: Filters VEP annotations based on transcript specifications
  • 🧩 Modular Design: Structured to facilitate reuse of core functionalities as a library in other projects
  • 🚀 Extensibility: Prepared for future extensions to include local installations of VEP and Variant Recoder
  • 📋 Output Customization: Users can specify the output format (JSON, CSV, TSV, VCF) with configurable field selection
  • 📈 Tabular Data Export: Provides CSV and TSV output with a "flatten by consequence" strategy for comprehensive variant analysis
  • 👨‍👩‍👧‍👦 PED File Support: Reads standard 6-column PED files to extract family structure and affected status information for inheritance analysis
  • 🧬 Inheritance Pattern Analysis: Automatically deduces potential inheritance patterns (de novo, autosomal dominant/recessive, X-linked) from multi-sample VCF files and family structure information
  • 🗂️ VCF Handling: Supports standard VCF file input and generation of annotated VCF output, preserving original headers and adding annotations to the INFO field
  • ⚡ Batch Request Chunking: Automatically splits large batches of variants into smaller chunks for API requests, ensuring compliance with Ensembl limits and efficient processing
  • 🔄 Exponential Backoff Retry: Implements automatic retry with exponential backoff for transient API errors, improving reliability when Ensembl services experience temporary issues
  • ⚙️ Configuration File Support: Allows users to provide parameters through a structured configuration file

Quick Start​

Get started with Variant-Linker in just a few commands:

# Install dependencies
npm install

# Analyze a single variant
node src/main.js --variant "rs6025" --output JSON

# Process a VCF file with inheritance analysis
node src/main.js --vcf-input sample.vcf --ped family.ped --calculate-inheritance --output VCF

Use Cases​

Variant-Linker is perfect for:

  • Clinical Genetics: Annotating variants from clinical sequencing data
  • Research: Batch processing of variants for population studies
  • Pipeline Integration: As a library component in larger bioinformatics workflows
  • Family Studies: Inheritance pattern analysis in family-based genetic studies
  • Variant Prioritization: Scoring and ranking variants based on custom criteria

Ready to get started? Check out our Installation Guide to begin using Variant-Linker in your projects.

🎯 Perfect for Research & Clinical Use​

Variant-Linker bridges the gap between research and clinical genetics by providing enterprise-grade annotation capabilities in an easy-to-use package.