GAMUT

GAMUT manages and compares high-throughput Single Nucleotide Polymorphism (SNP) variant data derived from Next Generation Sequencing to enable population-level variant comparison and genotype–phenotype analyses.

Key Features:

• Efficient SNP comparison: Generates probable lists of variants that differentiate two or more populations for applications such as array design, genotype imputation, and cataloging variants in regions of interest.
• Scalable architecture: Implements a client-server architecture with MongoDB as the backend database for scalable variant data management.
• Parallel data uploading: Uses Spark-based parallel data uploading to accelerate ingestion of large genomic datasets.
• Deployment options: Deployable on WildFly application servers and Docker containers for varied computational environments.
• Dynamic querying: Supports queries by free text, chromosome position, and gene name to retrieve subsets of variant data.
• Visualization outputs: Produces bar and pie charts and tabular formats for representing queried variant data.
• Export formats: Provides data export in text, HTML, and JSON formats.

Scientific Applications:

• Population genetics: Comparative analysis of SNP distributions between populations to identify differentiating variants.
• Array design: Selection of candidate SNPs for genotyping array content based on population differentiation.
• Genotype imputation support: Identification and cataloging of variants to inform imputation reference selection and evaluation.
• Region-specific variant cataloging: Aggregation and comparison of variants within genomic regions of interest for functional and association studies.
• Genotype–phenotype analysis: Facilitating exploration of variants potentially underlying phenotypic traits.

Methodology:

Processes SNPs from Next Generation Sequencing; generates probable population-differentiating variant lists; uses a client-server design with MongoDB backend; employs Spark-based parallel data uploading; supports text-, chromosome position-, and gene-name-based querying; produces bar/pie charts and tables and exports in text, HTML, and JSON; deployable on WildFly and Docker.