Rejoinder: "Gene Hunting with Hidden Markov Model Knockoffs"

Abstract

In this paper we deepen and enlarge the reflection on the possible advantages of a knockoff approach to genome wide association studies (Sesia et al., 2018), starting from the discussions in Bottolo & Richardson (2019); Jewell & Witten (2019); Rosenblatt et al. (2019) and Marchini (2019). The discussants bring up a number of important points, either related to the knockoffs methodology in general, or to its specific application to genetic studies. In the following we offer some clarifications, mention relevant recent developments and highlight some of the still open problems.