Schrödinger's Cat in Simulations in Genome-wide Association Studies

Simulations are essential components for testing methods or assumptions in genome-wide association studies (GWAS). We show through theory and examples that markers can be both causal and non-causal simultaneously, resulting in a paradox, had simulation not being run properly. We developed a software (ParaPheSim - a paradoxical phenotype simulator) that allows users to create different traits whose genetic correlation is exactly 1 and yet they have no genetic overlap.