GWAS Nextflow pipeline
A nextflow pipeline to perform genome-wide association studies (GWAS) using regenie. The pipeline takes files in BGEN (e.g. from UK Biobank) or VCF format (e.g. from Michigan Imputation Server) as an input and outputs association results, annotated tophits and an interactive HTML report including numerous plots (e.g. Manhattan Plot, QQ Plot) and statistics (e.g. phenotype histogram, top loci).
nf-gwas is available on GitHub.
Documentation can be found here.