API Reference

This section provides auto-generated documentation from the VariantCentrifuge source code.

Core Modules

• CLI Module
• Pipeline Module
• Configuration Module

Analysis Components

• Analyze Variants Module
• Gene Burden Module
• Statistics Module
• Scoring Module

Data Processing

• Filters Module
• Extractor Module
• Replacer Module
• Converter Module

Utilities and Helpers

• Utils Module
• Helpers Module
• Validators Module

Report Generation

• HTML Report Module
• IGV Report Module
• Links Module

Data Integration

• Phenotype Module
• Phenotype Filter Module
• Gene BED Module

Module Overview

Core Pipeline

• CLI Module - Command-line interface and argument parsing

• Pipeline Module - Main workflow orchestration and coordination

• Configuration Module - Configuration file loading and validation

Analysis & Statistics

• Analyze Variants Module - Variant-level analysis and gene burden testing

• Gene Burden Module - Statistical methods for gene burden analysis

• Statistics Module - Summary statistics and data aggregation

• Scoring Module - Custom variant scoring with configurable formulas

Data Processing

• Filters Module - SnpSift-based variant filtering operations

• Extractor Module - VCF field extraction utilities

• Replacer Module - Genotype replacement with sample IDs

• Converter Module - TSV to Excel conversion and formatting

Utilities

• Utils Module - Common utility functions and external tool integration

• Helpers Module - Data manipulation and processing helpers

• Validators Module - Input validation and sanity checking

Reporting

• HTML Report Module - Interactive HTML report generation

• IGV Report Module - IGV.js integration for genomic visualization

• Links Module - External database link generation

Data Integration

• Phenotype Module - Phenotype data loading and integration

• Phenotype Filter Module - Phenotype-based filtering operations

• Gene BED Module - Gene coordinate processing and BED file generation