For the last step, we chose COLOC to estimate the probability of colocalization of GWAS and eQTL signals. COLOC probabilities cluster more distinctly into different classes and thus, unlike other methods, suggests a natural cut off threshold at P = 0.5. Another advantage of COLOC is that for genes with low probability of colocalization, it further distinguishes distinct GWAS and eQTL signals from low power. This is a useful feature that future development of colocalization methods should also offer. SMR, on the other hand, uses its own estimate of “heterogeneity” of signals calculated by HEIDI.
