Although PAINTOR, CAVIAR and CAVIARBF are very useful methods for performing fine-mapping on GWAS summary data, we think that their implementation via an exhaustive search through all possible causal configurations is likely to hinder their use in several settings. For example, it becomes computationally slow or even impossible to run these methods by allowing more than three causal variants on dense genotype data with thousands of variants per region. Thus, these methods are unlikely to make full use of unprecedented statistical power to discern complex association patterns provided by ever increasing GWAS sample sizes and genome sequencing technologies.
