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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