added dependency for combinevariants

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala

@@ -53,6 +53,8 @@ class CombineVariants(val root: Configurable) extends Gatk {
       case Some("UNIQUIFY") | Some("PRIORITIZE") | Some("UNSORTED") | Some("REQUIRE_UNIQUE") | None =>
       case _ => throw new IllegalArgumentException("Wrong option for genotypeMergeOptions")
     }
+    deps :::= inputFiles.filter(_.getName.endsWith("vcf.gz")).map(x => new File(x.getAbsolutePath + ".tbi"))
+    deps = deps.distinct
   }
 
   override def cmdLine = super.cmdLine +

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -18,15 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsMerge, BcftoolsCall }
+import nl.lumc.sasc.biopet.core.{Reference, SampleLibraryTag}
+import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge}
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
-import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
-import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
-import org.broadinstitute.gatk.queue.function.CommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
+import nl.lumc.sasc.biopet.extensions.{Bgzip, Tabix}
+import nl.lumc.sasc.biopet.utils.Logging
+import org.broadinstitute.gatk.utils.commandline.Input
 
 /**
  * Common trait for ShivaVariantcalling