Wondering if anyone has reported this for the doc/sample file team:  Isn't the 
java config example line in that file wrong (at least for my java 1.6):

   <env id="_JAVA_OPTIONS">-Xmx=6GB</env>

With a setting of -Xmx=10g, Picard wouldn't run sortSam, instead this stderr 
Fatal error: Exit code 1 ()
Picked up _JAVA_OPTIONS: -Xmx=10g
Invalid maximum heap size: -Xmx=10g
Could not create the Java virtual machine.

I changed the <env> tag to take out "=" so it reads:

   <env id="_JAVA_OPTIONS">-Xmx6G</env>

and now its working fine!  Had to lookup -Xmx param format on the net from: 



Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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