diff --git a/playground/python/StressTestGATK.py b/playground/python/StressTestGATK.py
index 3eb7aabae..89abc7858 100755
--- a/playground/python/StressTestGATK.py
+++ b/playground/python/StressTestGATK.py
@@ -13,7 +13,7 @@ def usage():
 if __name__ == "__main__":
     opts = None
     try:
-        opts, args = getopt.getopt(sys.argv[1:], "f:c:", ["farm", "commands"])
+        opts, args = getopt.getopt(sys.argv[1:], "f:c:i", ["farm", "commands", "ignoreExistingFiles"])
     except getopt.GetoptError:
         print sys.argv
         usage()
@@ -21,12 +21,15 @@ if __name__ == "__main__":
 
     farm_sub = False
     commandsList = defaultCommands
+    ignoreExistingFiles = False
 
     for opt, arg in opts:
         if opt in ("-f", "--farm"):
             farm_sub = arg
         if opt in ("-c", "--commands"):
             commandsList = arg.split(',')
+        if opt in ("-e", "--ignoreExistingFiles"):
+            ignoreExistingFiles = True
 
     for line in open(args[0]):
         lane = line.strip()
@@ -36,9 +39,9 @@ if __name__ == "__main__":
         # convert the fasta
         for analysis in commandsList:
             output = filebase + '.' + analysis + '.output'
-            #if not os.path.exists(output):
-            cmd = "java -jar ~/dev/GenomeAnalysisTK/trunk/playground/java/dist/GenomeAnalysisTK.jar T=" + analysis + " I= " + lane + " R= /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta "
-            print cmd
-            farm_commands.cmd(cmd, farm_sub, output)
+            if ignoreExistingFiles or not os.path.exists(output):
+                cmd = "java -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar T=" + analysis + " I= " + lane + " R= /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta "
+                print cmd
+                farm_commands.cmd(cmd, farm_sub, output)