VarGen

VarGen automates retrieval, integration, and annotation of genetic variants from public databases to identify and characterize disease-associated variants.

Key Features:

• Automated Data Retrieval: Retrieves variant data from OMIM, FANTOM5, GTEx, and the GWAS catalog.
• Data Integration: Compiles and integrates retrieved variant datasets into a unified resource for downstream analysis.
• Customizable Input: Accepts an OMIM morbid ID and optional parameters such as lists of tissues or GWAS traits to focus queries.
• Variant Annotation: Annotates variants using aggregated data from the integrated databases to assess potential disease relevance.

Scientific Applications:

• Variant–disease relationship analysis: Aggregates and annotates disease-related variants to support analysis of variant–disease associations.
• Hypothesis generation and testing: Automates data retrieval and annotation across public databases to accelerate hypothesis generation and testing in genetic research.
• Genetic disorder studies: Enables focused investigation of genetic disorders using OMIM morbid IDs and tissue or GWAS trait filters.
• Disease mechanism and target discovery: Identifies candidate variants that may inform disease mechanisms and therapeutic target discovery.

Methodology:

Integrates and annotates variant data from multiple public databases using an OMIM morbid ID as input.