VEGAS on Helix
VEGAS (Versatile Gene-based Association Study) is a program for performing gene-based tests for association using the results from genetic association studies. It annotates SNPs to corresponding genes, produces a gene-based test statistic, and then uses simulation to calculate an empirical gene-based p-value. Vegas was developed by Jimmy Liu at the Queensland Institute of Medical Resarch, Australia.
By default, the program uses the HapMap2 CEU (Central Europeans, Utah) population to estimate patterns of linkage disequilibrium for each gene. Other ready-to-use HapMap populations are also available to download. A custom set of individuals can also be used if individual genotype information is available.
VEGAS was developed by Jimmy Liu at the Queensland Institute of Medical Research.
/usr/local/vegasYou can set your path to include the vegas executables by typing 'module load vegas', as in the example below.
How To Use
Example files can be copied from /usr/local/vegas. Sample session:
$ cp -r hapmapCEU example.txt /home/user/vegas $ module load vegas $ vegas example.txt -pop hapmapCEU -out example