We do not recommend the broad use of this procedure, because outlier loci may contain valuable information. In particular, if any SNP affects trait 1 without affecting trait 2 proportionally, this suggests that trait 1 is not causal for trait 2. An alternative explanation is that its effect on trait 2 is masked by an opposing pleiotropic effect, either of the same causal SNP or of a different causal SNP at the same locus. If an outlier locus is to be removed, we recommend manually examining it and determining whether its removal can be justified or whether it provides competing statistical evidence against a causal effect.
