High throughput sequencing has facilitated a precipitous drop in the cost of whole genome human DNA sequencing, prompting predictions of a revolution in medicine via personalization of diagnostic and therapeutic strategies to individual genetics. Disclosed is a comprehensive series of methods for identification of genetic variants and medical genotypes, phasing genetic data and using Mendelian inheritance for quality control, and providing predictive genetic information about risk for rare disease phenotypes and response to pharmacological therapy in single individuals and father-mother-child trios.