Help! I am trying to download GATK but when I do my computer says it does have a program to open the file...?
Have a look at this tutorial that may help you: http://gatkforums.broadinstitute.org/discussion/1200/howto-test-your-gatk-installation
Have you tried typing java -jar <path to GenomeAnalysisTK.jar> --help into you command line?
java -jar <path to GenomeAnalysisTK.jar> --help