VCPA

VCPA performs end-to-end processing of whole-genome (WGS) and exome (WES) sequencing data to align reads, call variants (including SNPs and Indels), and generate quality metrics for genomic studies such as the Alzheimer's Disease Sequencing Project.

Key Features:

• Pipeline component: Implemented in Workflow Description Language (WDL) to provide reproducible workflows.
• Sequencing support: Processes whole-genome sequencing (WGS) and exome sequencing (WES) data.
• Variant calling: Aligns raw sequence reads and calls variants using the Genome Analysis Toolkit (GATK).
• Cloud optimization: Optimized for execution on Amazon Elastic Compute Cloud (EC2) and cloud computing for scalable processing.
• Tracking database: Provides real-time monitoring of job status and visualization of over 100 quality metrics per genome.
• Compatibility: Functionally equivalent to the CCDG/TOPMed pipeline.
• Containerization: Distributed as a Dockerized solution for cloud deployment.

Scientific Applications:

• High-throughput genomics: Enables large-scale processing of WGS and WES datasets for population and disease studies.
• Variant discovery: Facilitates identification of single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels).
• Disease-focused studies: Supports genomic analyses for projects such as the Alzheimer's Disease Sequencing Project.
• Quality assessment: Enables assessment of sequencing data integrity using over 100 per-genome quality metrics.

Methodology:

Implemented in WDL, the pipeline aligns raw reads and performs variant calling with GATK, runs on cloud infrastructure (Amazon EC2) or Docker containers, and records and visualizes over 100 quality metrics per genome in a tracking database.