Described is a computer-implemented method (CIM) for simulating a population of offspring genomes from the genomes of the two individuals, while taking into account linkage disequilibrium. The CIM annotates each genome in the population of offspring genomes with disease variants from genomic databases that contain variant information on diseases that involve more than one gene, and predicts pathogenic variants in the annotated population of offspring genomes. The CIM performs a statistical analysis of the annotated population of offspring genomes to determine the probability of morbidity within the simulated offspring population and displays the results on a user interface for visualization.