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

  • Binary (case-control) phenotypes, single and multiple quantitative phenotypes
  • Bayesian and Frequentist tests
  • Ability to condition upon an arbitrary set of covariates and/or SNPs.
  • Various different methods for the dealing with imputed SNPs.

Accessing the software

To load the module:

$ module load apps/snptest/2.5.2

To view command-line options, run the following command:

$ snptest_v2.5.2 -help

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the SNPTEST website for more information regarding this application.

Last modified: 14 September 2017