BIGwas GWAS Association Testing Pipeline

BIGwas GWAS Association Testing Pipeline performs automated quality control and association testing for large-scale genome-wide (GWAS) and phenome-wide (PheWAS) studies to detect genotype–phenotype associations across population-based biobanks.

Key Features:

• Automation and Scalability: Automates quality control (QC) and association testing for binary and quantitative trait GWAS across large cohorts, supporting datasets approaching one million samples.
• Portability and Reproducibility: Implements Nextflow workflow management and Singularity containers to ensure reproducible execution across computing platforms.
• Dynamic Parallelization: Employs dynamic parallelization optimized for HPC environments; in one reported example it processed 974,818 individuals and 92 million genetic markers in approximately 16 days using seven compute nodes.

Scientific Applications:

• Large-scale GWAS and PheWAS: Enables genome-wide association and phenome-wide scans across population-based biobanks to identify genotype–phenotype associations.
• Multi-cohort Analyses: Supports multi-cohort GWAS analyses involving up to one million samples.
• PheWAS Resource Generation and Cross-population Studies: Facilitates generation of genome-wide PheWAS resources and exploration of genetic associations across diverse populations and traits.

Methodology:

Integrates quality control measures and association testing protocols within a Nextflow-managed workflow using Singularity containers and dynamic parallelization for high-performance computing.