nf-gwas

nf-gwas performs highly parallelized and reproducible genome-wide association studies (GWAS) on biobank-scale data using an automated Nextflow pipeline that integrates regression modeling and comprehensive reporting.

Key Features:

• Automated Pre- and Post-Processing: The pipeline automatically performs numerous pre- and post-processing steps for GWAS analysis.
• Regression Modeling Integration: It integrates regression modeling from the REGENIE package for statistical analysis.
• Multiple Testing Modes: It supports single-variant, gene-based, and interaction testing.
• Interactive Reporting: It includes extensive reporting functionality with interactive Manhattan plots inspectable directly in the web browser.
• Unit-Style Testing: The pipeline is tested using the nf-test framework, a requirement for clinical and pharmaceutical settings.
• Validation and Benchmarking: It has been validated against published GWAS datasets and benchmarked on high-performance computing and cloud infrastructures.

Scientific Applications:

• Biobank-Scale GWAS: It enables detection of novel genotype-phenotype relationships in large-scale genetic datasets.
• Multi-Phenotype Analysis: It allows researchers to inspect thousands of phenotypes simultaneously.
• Cloud and HPC Genomics: It provides scalable GWAS analysis with cost estimations for high-performance computing and cloud deployments.

Methodology:

The pipeline is built in Nextflow and integrates regression modeling from the REGENIE package. It performs automated pre- and post-processing steps and has been validated against published GWAS datasets.