VarAnnote v1.0.8 Documentation
VarAnnote is a comprehensive variant analysis and annotation suite designed for genomic research and clinical applications. This production-ready tool provides advanced filtering, configuration management, and integration with multiple genomic databases.
🚀 Key Features
Advanced Filtering System - 13 filter operators with predefined filter sets
Configuration Management - YAML-based configuration with environment variable support
Database Integration - Support for ClinVar, gnomAD, dbSNP, COSMIC, and more
Async API System - High-performance API calls with rate limiting
Multiple Output Formats - JSON, CSV, TSV, VCF, Excel, XML, Parquet
Professional CLI - Comprehensive command-line interface
High Test Coverage - 82% test coverage with 394+ tests
📦 Quick Installation
pip install varannote
🔧 Basic Usage
from varannote.core.annotator import VariantAnnotator
from varannote.utils.config_manager import ConfigManager
# Load configuration
config = ConfigManager()
# Initialize annotator
annotator = VariantAnnotator(config)
# Annotate variants
results = annotator.annotate_vcf("variants.vcf")
📚 Documentation Sections
User Guide:
API Reference:
🔗 Links
GitHub Repository: https://github.com/AtaUmutOZSOY/VarAnnote
PyPI Package: https://pypi.org/project/varannote/
Issue Tracker: https://github.com/AtaUmutOZSOY/VarAnnote/issues
📄 License
This project is licensed under the MIT License.