SNPTest
Overview
SNPTest 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.
Restrictions on use
All users may access and use SNPTest. The software is (c) 2007, The University of Oxford.
Running the application
Please do not run SNPTest commands on the login node. qrsh is recommended for some commands. Computationally intense work should be done via the batch system.
Examples
The following example first runs SNPTest as a serial job.
#!/bin/bash --login #$ -S /bin/bash #$ -cwd module load apps/binapps/snptest/2.5.2 snptest \ -summary_stats_only \ -data $SNPTESTDIR/example/cohort1.gen $SNPTESTDIR/example/cohort1.sample $SNPTESTDIR/example/cohort2.gen $SNPTESTDIR/example/cohort2.sample \ -o ex.out
and submit the job using qsub jobscript where jobscript is the name of your job script file.