welch16/gwas_vitamind_african_ancestry

Code for the "Genome-wide association study (GWAS) and functional analysis of genetic variants associated with circulating vitamin D binding protein in African Americans # Genome-wide association study (GWAS) of circulating vitamin D outcomes among individuals of African ancestry L Parlato, R Welch, IM Ong, J Long, L Cai, MD Steinwandel, WJ Blot, W Zheng, S Warren Andersen, _"Genome-wide association study (GWAS) of circulating vitamin D outcomes among individuals of African ancestry"_ (2023), The American Journal of Clinical Nutrition, 117-2, 308-316 The directory structure is: - `01_quality_control/` - QC manipulations to get a first dataset - `02_merge_imputation/` - All manipulations to impute the different cohorts, and then join the imputed results to build a full genotype dataset. - `03_gwas_analysis/` - Data analysis presented in the manuscript --- The requirements to use this are: - HTCondor v8.6.13 - PLINK v1.9 - PLINK2 v2.0 - Minimac4 v1.0.1 - R v4.0.2 ---