SNPTEST is a program for the analysis of single SNP association in genome-wide studies. The tests implemented include

The program is designed to work seamlessly with the output of our genotype imputation software IMPUTE [1] and the programs QCTOOL and GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC) [2]. Much of the theory behind the implemented tests is described in this paper [3].

SNPTEST has many different features which are illustrated below through a number of different examples that use the datasets provided with the software in the directory example/. These files contain data at 200 SNPs on 1000 individuals that are split into a control cohort and a case cohort. These datasets can be used to try out the tests using both binary (case-control) and quantitative phenotypes.

The latest stable version of SNPTEST is v2.5.2. Changes in this release include bug fixes and enhancements as documented here. To get started, download a pre-built binary for your platform from the download page and run an example command.


To contact us, please use the OXSTATGEN mailing list - see here for details.


The following people contributed to the design and development of SNPTEST: