VEGAS (Versatile Gene-based Association Study) is a free program for performing gene-based tests for association using the results from genetic association studies. After reading in SNP association p-values, it will annotate SNPs according to their position in genes, produce a gene-based test statistic, and then use simulation to calculate an empirical gene-based p-value.
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Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, Brown KM, AMFS Investigators, Hayward NK, Montgomery GW, Visscher PM, Martin NG, MacGregor S. (2010).
A Versatile Gene-Based Test for Genome-wide Association Studies.
American Journal of Human Genetics, 87.