diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index a3204c20f2713a8ddbba0e67399bf9a29b495b01..b807145a61d9adbfef7f71281a720ed5242f2cf4 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -20,7 +20,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
 
 /**
  * Extension for pindel
@@ -47,10 +47,10 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
   var input: File = _
 
   @Argument(doc = "The pindel configuration file")
-  var pindel_file: Option[File] = _
+  var pindel_file: Option[File] = None
 
   @Argument(doc = "Configuration file with: bam-location/insert size/name")
-  var config_file: Option[File] = _
+  var config_file: Option[File] = None
 
   @Argument(doc = "Work directory")
   var output_prefix: File = _
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
index 0bccf63d853db3b1f5c8c1129ab1daffd60c82cc..0e0aed54fade24fb0589d2a65ca2416f7ef363fa 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -32,7 +32,7 @@ class Pindel(val root: Configurable) extends SvCaller {
     for ((sample, bamFile) <- inputBams) {
       val pindelDir = new File(outputDir, sample)
 
-      val config_file: File = new File(bamFile.getAbsolutePath + ".pindel.cfg")
+      val config_file: File = new File(outputDir + "." + sample + ".pindel.cfg")
       val cfg = new PindelConfig(this)
       cfg.input = bamFile