--- a/tool_dependencies.xml	Tue Nov 26 06:10:20 2013 -0500
+++ b/tool_dependencies.xml	Sat Nov 30 10:36:47 2013 -0500
@@ -4,6 +4,10 @@
         <environment_variable action="set_to" name="GATK2_PATH">/please set the path to your GATK2 dir in the corresponding env.sh file/</environment_variable>
     </set_environment>
     <!-- 
+    Use GATK2_SITE_OPTIONS to set additional parameters that should be inserted in every GATK2 call.
+    The intended use case was to prohibit GATK2 to collect and send data.
+    For example:
+    
     -et "NO_ET" -K "/data/gatk2_key_file" ##ET no phone home
     -->
     <set_environment version="1.0">