CLI Usage Guide

VarAnnote provides a comprehensive command-line interface for variant annotation.

Basic Commands

Annotate VCF File

varannote annotate input.vcf --output results.json

Apply Filters

varannote annotate input.vcf --filter high_confidence --output filtered.json

Multiple Filters

varannote annotate input.vcf --filter rare_variants,high_confidence --output results.json

Output Formats

# JSON output (default)
varannote annotate input.vcf --output results.json

# CSV output
varannote annotate input.vcf --output results.csv --format csv

# Excel output
varannote annotate input.vcf --output results.xlsx --format excel

Advanced Options

Configuration File

varannote annotate input.vcf --config custom_config.yaml

Database Selection

varannote annotate input.vcf --databases clinvar,gnomad

Batch Processing

varannote batch-annotate *.vcf --output-dir results/

Help and Version

# Show help
varannote --help
varannote annotate --help

# Show version
varannote --version