Chunk #3 — METHODS AND MATERIALS — Simulation and Recovery of SNP Heritability for Binary Traits — Data Generating Model.

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Pervasive Downward Bias in Estimates of Liability-Scale Heritability in Genome-wide Association Study Meta-analysis: A Simple Solution.

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The bivariate LDSC intercept, expressed as ρ1,2Ns1,2N1N2 for cohorts 1 and 2, was 0 owing to setting the sample overlap (Ns) to 0 for all simulations. GWAS z statistics were simulated following the equation above and using the mvrnorm R function from the MASS package for each SNP. For each condition, 100 sets of summary statistics were simulated (i.e., 1000 cohort-level summary statistics per condition for a total of 11,000 simulated cohorts across the 11 conditions).