Question received via email:

I am currently carrying out association analyses with the GENESIS package. I just wanted to know if there is a reason for the removing of the Wald test option in version 2.16.0. Would you recommend not to use the older versions (and thus the Wald test statistics) of the package for genotype association tests anymore?

The Wald test done in previous versions of GENESIS was actually an approximation to the Wald test based on the Score test, not an exact Wald test. Because the underlying code of the Score and Wald tests was nearly identical, the only meaningful difference was that the Wald test would return effect size estimates (Est). The same effect size estimates from this approximation are still available in the new output as the "Est" column. We made this change to improve the clarity of what was actually being reported in the results, and to simplify the code. While we always recommend upgrading to the current version of the code for new analyses, results using older versions of the package (with either the Score or Wald test) are still perfectly valid.