Genome Wide Association Study pipeline (GWASpi)

Genome Wide Association Study pipeline (GWASpi) processes and analyzes single nucleotide polymorphism (SNP) array data to support genome-wide association studies aimed at identifying genetic loci associated with traits.

Key Features:

• SNP array data management and analysis: Manages and analyzes single nucleotide polymorphism (SNP) array data for GWAS workflows.
• Implementation technologies: Implemented in Java and using Apache-Derby and NetCDF-3 for data storage and handling.
• Workflow integration: Integrates common analysis tools used in GWAS workflows to enable end-to-end data processing and result generation.
• Computational efficiency: Leverages database technologies to optimize data handling and reports reductions in processing time by up to two orders of magnitude.
• Error reduction: Minimizes errors associated with data parsing and manipulation to improve reliability of study outcomes.

Scientific Applications:

• Genetic locus discovery: Identification of genetic loci associated with human traits using SNP arrays in genome-wide association studies.
• Genomic research and clinical studies: Support for basic genomic research and translational or clinical GWAS investigations.

Methodology:

Uses database technologies (Apache-Derby, NetCDF-3) within a Java implementation to optimize data handling and integrates common GWAS analysis tools.