Association Viewer

Association Viewer visualizes SNPs and genomic annotations to contextualize genome-wide association study (GWAS) results and related genetic variation.

Key Features:

• Genomic context visualization: Displays SNPs and other genetic variants alongside gene annotations, linkage disequilibrium (LD) plots, and user-supplied datasets within genomic regions.
• Data integration: Retrieves gene annotations from Ensembl and LD data from HapMap for use in analyses.
• Custom data import: Accepts user tracks in BED and WIG file formats to incorporate custom datasets.
• Efficient data handling: Implements on-the-fly downloading of supplementary data with local caching to reduce redundant retrieval.
• Track operations: Supports aggregation and intersection of multiple data tracks for comparative analyses across regions.
• Scalability: Handles very large-scale genomic datasets for high-throughput genetic studies.
• Cross-platform compatibility: Implemented in Java and reported to run on Microsoft Windows XP, MacOSX, and GNU/Linux.

Scientific Applications:

• GWAS interpretation: Visualizes association signals to aid identification of candidate genes and interpretation of genomic architecture underlying trait associations.
• Genomic research: Enables detailed examination of genetic variation for applications in functional genomics, population genetics, and evolutionary biology.
• Custom data analysis: Integrates user-provided tracks to support hypothesis-driven exploration and analysis of specific datasets.

Methodology:

Implemented in Java; retrieves Ensembl gene annotations and HapMap LD data, imports BED and WIG files, implements on-the-fly data download with local caching, and supports aggregation or intersection of multiple data tracks.