diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index 1cbddafe6b999ded0579608de75c35e136f4a053..127f2991608612f105fcfe81e3cea2048262f1b4 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -5,6 +5,10 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
   executable = "java"
 
+  javaGCThreads = config("java_gc_threads")
+  javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
+  javaGCTimeLimit = config("java_gc_timelimit")
+
   override def afterGraph {
     memoryLimit = config("memory_limit")
   }