Gatk java

From the GATK web site GATK troubleshooting,

Make sure that your Java version is at least 1.6, by typing the following command:

java -version

Expected Result

You should see something similar to the following text:

java version "1.6.0_12"
Java(TM) SE Runtime Environment (build 1.6.0_12-b04)
Java HotSpot(TM) 64-Bit Server VM (build 11.2-b01, mixed mode)

We should not update to 1.7 according to these threads 1 2

GATK needs java 1.6

update 5 Sept. 2013

from GATK from GATK 2.5 java 7 will be needed