Quick Start Guide

5-Minute Setup

1. Install VarAnnote

pip install varannote

2. Basic Usage

from varannote.core.annotator import VariantAnnotator

# Initialize annotator
annotator = VariantAnnotator()

# Annotate a VCF file
results = annotator.annotate_vcf("your_variants.vcf")

# Save results
annotator.save_results(results, "annotated_variants.json")

3. CLI Usage

# Annotate VCF file
varannote annotate input.vcf --output results.json

# Apply filters
varannote annotate input.vcf --filter high_confidence --output filtered.json

Example Workflow

from varannote.core.annotator import VariantAnnotator
from varannote.utils.filters import FilterSet

# Create annotator
annotator = VariantAnnotator()

# Create filter for rare, high-confidence variants
filter_set = FilterSet()
filter_set.add_predefined("rare_variants")
filter_set.add_predefined("high_confidence")

# Annotate and filter
results = annotator.annotate_vcf("variants.vcf", filters=filter_set)

# Export to multiple formats
annotator.export_csv(results, "results.csv")
annotator.export_excel(results, "results.xlsx")