diff --git a/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index c3f325c71..64fe01628 100644
--- a/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -104,7 +104,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         }
 
         engine.setSafetyChecking(! UNSAFE.toLowerCase().equals("true"));
-        engine.setSortOnFly(! ENABLED_SORT_ON_FLY.toLowerCase().equals("true"));
+        engine.setSortOnFly(ENABLED_SORT_ON_FLY.toLowerCase().equals("true"));
 
         engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true"));
         //engine.testReference();