Supplementary Figure 11: GWAS summary simulations using haplotype-copying model of population.
From: Integrative approaches for large-scale transcriptome-wide association studies
Results from simulations matching Supplementary Figure 4 re-analyzed using HAPGEN2 to generate all GWAS sub-study individuals. After holding out 1,000 samples for the expression reference, SHAPEIT2 was used to phase 5,000 individuals in a cis-block for each of 100 random genes, yielding 100 random reference panels. For each reference panel we used HAPGEN to generate 60 sub-studies of 5,000 individuals using its haplotype-copying model (under neutrality). Phenotypes were generated with the same causal variants and effects for each sub-study, and the corresponding GWAS summary statistics were computed by meta-analyzing across these batches. Default parameters for SHAPEIT and HAPGEN were always used, and the appropriate genetic map was downloaded from the SHAPEIT2 website.
