Sequence Kernel Association Test (SKAT)

Check this box to perform the Sequence Kernel Association Test (SKAT) defined by Wu et al. (2011)1Wu, M.C., S. Lee, et al. (2011). Rare-variant association testing for sequencing data with the sequence kernel association test. American Journal of Human Genetics 89:82-93..

In this test, the variance component for all SNPs (or collapsed rare variant loci) with the same value of the Annotation Analysis Group Variable is tested for using a score statistic that follows a linear combination of chi-square distributions.

Important: This method can be used with continuous and binary traits only.

The chi-square approximation given by Liu, Tang, and Zhang (2009)2Liu, H., Y. Tang, and H.H. Zhang. (2009). A new chi-square approximation to the distribution of non-negative definite quadratic forms in non-central normal variables. Computational Statistics and Data Analysis 53:853-856.http://dx.doi.org/10.1016/j.csda.2008.11.025 is used to calculate p-values for this test.

Note: Random effects are ignored for this test.

To Perform the SKAT Test:

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Check the box.