To speed computations, instead of simulating data and then estimating effect sizes, we directly generated effect-size estimates by adding multivariate-normally-distributed noise to the simulated effect sizes. The variance of the noise for each trait was determined by the assumed GWAS expected χ2-statistics, and the covariance of the noise between the traits was determined by the assumed GWAS expected χ2-statistics and correlation of GWAS estimation error across traits.
