This document is a user manual for PODKAT, an R package implementing non-burden association tests for rare and private variants, most importantly, the position-dependent kernel association test (PODKAT). It provides a gentle introduction into how to use PODKAT. Not all features of the R package are described in full detail. Such details can be obtained from the documentation enclosed in the R package. Further note the following: (1) this is not an introduction to statistical genetics or association testing; (2) this is not an introduction to R or any of the Bioconductor packages used in this document; (3) this is not an introduction to statistical hypothesis testing or probability theory. If you lack the background for understanding this manual, you first have to read introductory literature on the subjects mentioned above. All R code in this document is written to be runnable by any user. However, some of the code chunks require the download of external files, require an Internet connection, or require too much computation time to be runnable when the package is built, checked, or installed. The output lines of R code chunks that are not actually executed when processing this document are marked with '##!!##' and, in case that the user needs to perform extra steps to execute the code, these steps are listed explicitly.