This is a software pipeline based on PLINK for Genome-Wide Association Studies (GWAS). A linear or logistic regression can be conducted in order to identify genetic variants being associated with a quantitative or a binary trait. The pipeline also includes two methods (GCTA-COJO and PLINK-CLUMP) for the identification of independent genetic variants, i.e. variants which are in linkage equilibrium. It is presumed that the scripts can be installed and run on a high-performance computer (HPC) with the “Simple Linux Utility for Resource Management” (SLURM) workload manager installed.