corresponding genotypes for the SNP at the locus. For simulations that required loci greater than 10 KB, we instead drew Z-scores from a Multivariate Normal distribution with covariance equal to LD based on the European 1 KG and non-centrality parameters at causal sites drawn from a Normal distribution with mean 5 and standard deviation 0.2. When measuring performance of our simulations, we examine the proportion of causal SNPs identified as a function of the average number of SNPs per locus selected for follow-up restricted to loci that contain at least one causal variant (we show in Figure S7 that using Positive Predictive Value as a metric of accuracy attains qualitatively similar results).
