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VEGAS 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.
Vegas project page: http://gump.qimr.edu.au/VEGAS/
The following Modules files should be loaded for this package:
module load VEGAS/VEGAS-0.8