VarGenius

VarGenius performs variant calling, annotation, and cohort-level management of DNA sequencing data from whole-exome sequencing (WES) and targeted panels, enabling joint analysis and structured storage of variant and sample metadata for downstream genetic studies.

Key Features:

• Customizable Pipelines: Supports customizable analysis pipelines for WES and targeted panel datasets.
• Parallel Computing Capabilities: Leverages parallel computing and has been tested on a high-performance cluster of 52 machines with 120 GB RAM each.
• Integration with GATK Best Practices: Implements GATK best practices for germline variant calling.
• Variant Annotation via Annovar: Annotates called variants using Annovar.
• Joint Analysis: Performs joint analysis of hundreds of samples with a single command.
• Database Integration: Stores calling quality statistics, variant annotations, allelic frequencies, personal data, genotypes, and phenotypes in a dedicated database.
• Output Formats: Exports results in tabular and XLS file formats.
• Scalability and Performance: Processes a 50M WES family analysis in approximately 7 hours and a joint analysis of 30 WES samples in about 24 hours.
• Input Data: Accepts FASTQ files as input for downstream processing.

Scientific Applications:

• Mendelian disease research: Supports identification of causative mutations in Mendelian disease studies using targeted resequencing and WES.
• Diagnostic and research sequencing: Enables diagnostic and research workflows for variant discovery and interpretation.
• Genetic epidemiology and population genetics: Facilitates large-cohort analyses for genetic epidemiology and population genetics studies.

Methodology:

Processes FASTQ input through a GATK-based pipeline for variant calling, annotates variants with Annovar, and stores results and associated metrics and metadata in a dedicated database.