KATE is a program that employs hierarchical clustering and kernel based association testing to analyse the effects of low frequency and rare variants on quantitative traits within a chromosomal region.

Single-point analysis of low-frequency and rare variants is under-powered, as not enough copies of the minor allele are observed. An alternative approach is to use methods that combine information across multiple low frequency or rare variant sites within a region. Focusing on the analysis of quantitative traits, we developed KATE (Kernel Association Test Extended) that uses the Allele Match kernel to cluster individuals into disjoint clusters and tests the cluster-specific effects via ANOVA.

Download and Installation

System requirements

The software should run on any UNIX or GNU/Linux system.

Download KATE

After downloading the files, please read the KATE_README.txt file to set up and run the file.


If you have any problems running KATE, then please contact either Ioanna Tachmazidou or Eleftheria Zeggini.

It is recommended that you contact the author of KATE, Ioanna Tachmazidou regarding bugs or problems running the script.


Sanger Contributors


  • Rare variant association testing for next-generation sequencing data via hierarchical clustering.

    Tachmazidou I, Morris A and Zeggini E

    Human heredity 2012;74;3-4;165-71

Tool Type