A PRIMER ON GENOTYPE IMPUTATION

Abstract

Haplotype phasing and genotype imputation have become commonly used for genetic studies of all types, but especially for genome wide association studies and as a tool in plant breeding programs. As the ability of labs of all sizes to implement genome wide association studies increases, the skills and knowledge needed for preparing these data must be more commonly taught to students through all levels of higher education. This document is meant to serve as an introduction to the underlying concepts and show an example of the basic implementation and troubleshooting of haplotype phasing and genotype imputation for genetic studies.