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Program for frequentist and Bayesian tests of single-nucleotide polymorphism (SNP) association with binary (case-control) and quantitative phenotypes taking genotype uncertainty into account.

The software is part of the Oxford genome-wide analysis software suite (OGWASS).

SNPTEST 2 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

The program is designed to work seamlessly with the output of our genotype imputation software IMPUTE 4 and the programs QCTOOL and GTOOL.

Commercial licence is available as part or whole of our software suite, OGWASS.

The SNPTEST 2 program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC).

Much of the theory behind the implemented tests is described in the technical report ‘A new multipoint method for genome-wide association studies via imputation of genotypes’.

SNPTEST is listed as Oxford University Innovation project 003589.

SNPTEST2 is listed as Oxford University Innovation project 007695.

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