gPLINK

gPLINK provides Java-based integration with PLINK to facilitate execution and management of whole-genome association study analyses.

Key Features:

• Java-based implementation: Implements a Java-based integration layer for interacting with PLINK command execution and project-level management.
• Command Management: Maintains a comprehensive record of all executed PLINK commands within a project to support reproducibility.
• File Tracking: Tracks input and output files associated with each command to preserve data provenance.
• Annotation Capabilities: Supports annotation of PLINK result files to enhance result interpretability.
• Integration with Haploview: Facilitates integration with Haploview for linkage disequilibrium and haplotype analysis.
• PLINK functionality exposure: Exposes PLINK capabilities for data management, summary statistics, population stratification, association analysis, and IBD estimation.

Scientific Applications:

• Whole-Genome Association Studies: Supports manipulation and analysis of large genotype datasets comprising hundreds of thousands of markers across thousands of individuals using PLINK commands.
• Population-based linkage analysis: Enables use of identity-by-descent information to map disease loci containing multiple rare variants.

Methodology:

Invokes PLINK functionality across five domains: data management; summary statistics; population stratification using identity-by-state (IBS) and identity-by-descent (IBD); association analysis; and IBD estimation for population-based linkage analysis to map disease loci containing multiple rare variants.