Regarding our collapsing PheWAS analyses, construction of the full set of genotype and phenotype matrices took 13,000 and 30 CPU hours to compile, respectively. The preprocessing steps such as rebalancing sex-specific case–control ratios are incorporated in the phenotype matrix construction time. Subsequently, the approximately 4.5 billion collapsing analysis statistical tests were calculated in 19,000 CPU hours. In wall-clock hours, this took 30 h to generate all the collapsing and phenotype matrices. Once the intermediate files were ready, the roughly 4.5 billion collapsing statistical tests took 8 h to complete.
