vtools

vtools provides storage, annotation, and analysis of genetic variants derived from next-generation sequencing (NGS) projects to support variant tracking and reanalysis.

Key Features:

• Integration with existing tools: Integrates with established bioinformatics software such as GATK, ANNOVAR, and BEDTools for cohesive annotation and analysis workflows.
• Variant storage: Stores genetic variant records and associates them with their originating samples.
• Variant annotation: Annotates variants using multiple annotation sources.
• Variant filtering: Supports filtering of variants for downstream analyses.
• Sample-variant tracking and reanalysis: Tracks variants in conjunction with their respective samples and supports dynamic updates and reanalysis.
• Multi-format and scalable data handling: Handles diverse data formats and large volumes typical of NGS projects.
• Sample-level analysis: Performs comprehensive analyses on underlying sample data.

Scientific Applications:

• Large-scale exome sequencing: Manages and annotates variants from large-scale exome sequencing projects.
• Variant management from alignments: Manages genetic variant data obtained from sequence alignments.
• Sample-level discovery: Enables comprehensive sample-level analyses to investigate genetic variation and its biological implications.
• Method development: Provides a foundation for developing more sophisticated analytical methods built on variant and sample data.

Methodology:

Performs variant storage, annotation, filtering, and sample-variant tracking; supports dynamic updates and reanalysis; and integrates with GATK, ANNOVAR, and BEDTools.