# Rejoinder: "Gene Hunting with Hidden Markov Model Knockoffs"

## TL;DR

This paper discusses the potential benefits and challenges of applying the knockoff methodology, specifically Hidden Markov Model knockoffs, to genome-wide association studies, emphasizing recent developments and open issues.

## Contribution

It provides a detailed reflection on the advantages, limitations, and recent progress of using knockoff methods in genetic research, especially in GWAS.

## Key findings

- Clarifies the advantages of knockoff methods in GWAS
- Highlights recent methodological developments
- Identifies open problems and future directions

## 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.