UKB Exome Analysis Pipeline

A Nextflow pipeline for running genome-wide association studies (GWAS) on UK Biobank exome sequencing data using REGENIE on the Research Analysis Platform (RAP).

Overview

This pipeline performs:

1. Genotype QC - Merges chromosomal data and applies quality control filters
2. Association Testing - Runs REGENIE two-step analysis for exome variants
3. Post-processing - Prepares results for downstream analysis including BHR and visualization

Quick Start

1. Configure Parameters

Edit config.sh to set your data paths and output directories.

2. Run Genotype Pipeline

nextflow run genotype_pipeline.nf

3. Run ExomeWAS Analysis

nextflow run exomWAS_pipeline/exome_was.nf \
    --pheno_desc_file your_phenotypes.txt \
    --output_dir results/

Pipeline Components

• genotype_pipeline.nf - Chromosome merging and SNP QC
• exomWAS_pipeline/ - Main REGENIE association analysis
• postanalysis/ - BHR preprocessing and result processing
• scripts/ - Utility scripts for data management

Requirements

• Nextflow
• Access to UK Biobank RAP
• Python 3.x with pandas, numpy
• R with required packages
• REGENIE software

Output

The pipeline generates:

• Association statistics per chromosome
• QC metrics and logs
• BHR-ready formatted files
• Manhattan plots and visualizations

Support

For issues or questions about this pipeline, please refer to the individual README files in each subdirectory for detailed usage instructions.