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")
   }
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
index 43ab44f4ec50499cfc4b77fdf5aae61a7ec7b939..398393f98605cffea9df5804f90d06932080324f 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
@@ -6,7 +6,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 class SamToFastq(val root: Configurable) extends Picard {
   javaMainClass = "picard.sam.SamToFastq"
-  javaGCThreads = config("gcthreads", default = 2)
 
   @Input(doc = "The input SAM or BAM files to analyze.", required = true)
   var input: File = _