diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 928f14329ef0747da3f1d7652c35beb560d9751d..e04af3d5b469330e9f0b72f0f265dd0d50004086 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -54,29 +54,43 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   }
 
   protected def checkExecutable {
-    try if (executable != null) {
-      val buffer = new StringBuffer()
-      val cmd = Seq("which", executable)
-      val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
-      if (process.exitValue == 0) {
-        executable = buffer.toString
-        val file = new File(executable)
-        executable = file.getCanonicalPath
-      } else {
-        logger.error("executable: '" + executable + "' not found, please check config")
-        throw new QException("executable: '" + executable + "' not found, please check config")
+    if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
+      try if (executable != null) {
+        if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
+          val oldExecutable = executable
+          val buffer = new StringBuffer()
+          val cmd = Seq("which", executable)
+          val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
+          if (process.exitValue == 0) {
+            executable = buffer.toString
+            val file = new File(executable)
+            executable = file.getCanonicalPath
+          } else {
+            logger.error("executable: '" + executable + "' not found, please check config")
+            throw new QException("executable: '" + executable + "' not found, please check config")
+          }
+          BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
+          BiopetCommandLineFunctionTrait.executableCache += executable -> executable
+        } else {
+          executable = BiopetCommandLineFunctionTrait.executableCache(executable)
+        }
+
+        if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
+          val is = new FileInputStream(executable)
+          val cnt = is.available
+          val bytes = Array.ofDim[Byte](cnt)
+          is.read(bytes)
+          is.close()
+          val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
+          BiopetCommandLineFunctionTrait.executableMd5Cache += executable -> temp
+        }
+
+        addJobReportBinding("md5sum_exe", BiopetCommandLineFunctionTrait.executableMd5Cache(executable))
+      } catch {
+        case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
       }
-
-      val is = new FileInputStream(executable)
-      val cnt = is.available
-      val bytes = Array.ofDim[Byte](cnt)
-      is.read(bytes)
-      is.close()
-      val md5: String = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
-
-      addJobReportBinding("md5sum_exe", md5)
-    } catch {
-      case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
+    } else {
+      addJobReportBinding("md5sum_exe", BiopetCommandLineFunctionTrait.executableMd5Cache(executable))
     }
   }
 
@@ -138,4 +152,6 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
 object BiopetCommandLineFunctionTrait {
   import scala.collection.mutable.Map
   private val versionCache: Map[String, String] = Map()
+  private val executableMd5Cache: Map[String, String] = Map()
+  private val executableCache: Map[String, String] = Map()
 }
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
index 943039fd7ece4f8c22ca07ce46f8d614c5631e80..c650581321a3db119ed524f9d71c596b90fb2151 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
@@ -1,6 +1,8 @@
 package nl.lumc.sasc.biopet.core
 
+import java.io.File
 import java.util.Properties
+import nl.lumc.sasc.biopet.core.config.Config
 import org.apache.log4j.Logger
 
 object BiopetExecutable extends Logging {
@@ -35,6 +37,7 @@ object BiopetExecutable extends Logging {
       nl.lumc.sasc.biopet.tools.SageCountFastq,
       nl.lumc.sasc.biopet.tools.SageCreateLibrary,
       nl.lumc.sasc.biopet.tools.SageCreateTagCounts,
+      nl.lumc.sasc.biopet.tools.MergeAlleles,
       nl.lumc.sasc.biopet.tools.SamplesTsvToJson)
   )
 
@@ -88,6 +91,14 @@ object BiopetExecutable extends Logging {
         println("version: " + getVersion)
       }
       case Array(module, name, passArgs @ _*) => {
+        // Reading config files
+        val argsSize = passArgs.size
+        for (t <- 0 until argsSize) {
+          if (passArgs(t) == "-config" || args(t) == "--config_file") {
+            if (t >= argsSize) throw new IllegalStateException("-config needs a value")
+            Config.global.loadConfigFile(new File(passArgs(t + 1)))
+          }
+        }
         getCommand(module, name).main(passArgs.toArray)
       }
       case Array(module) => {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 015c48dd1525dde3e91d49099a7e48f89c709e69..cf4ee286b0a7c40aa128f3d1fc807e8badce9515 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
 import org.broadinstitute.gatk.utils.commandline.Argument
 import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.function.QFunction
@@ -25,7 +25,6 @@ trait BiopetQScript extends Configurable {
   var functions: Seq[QFunction]
 
   final def script() {
-    for (file <- configfiles) globalConfig.loadConfigFile(file)
     if (!outputDir.endsWith("/")) outputDir += "/"
     init
     biopetScript
@@ -33,7 +32,7 @@ trait BiopetQScript extends Configurable {
       case f: BiopetCommandLineFunctionTrait => f.afterGraph
       case _                                 =>
     }
-    val configReport = globalConfig.getReport
+    val configReport = Config.global.getReport
     val configReportFile = new File(outputDir + qSettings.runName + ".configreport.txt")
     configReportFile.getParentFile.mkdir
     val writer = new PrintWriter(configReportFile)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
index 9b8197de1acdc1ca492760b931180e09176068bb..32977c6f615aa3cfda69539afee31c330d8e418a 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
@@ -7,9 +7,13 @@ import org.apache.log4j.WriterAppender
 import org.apache.log4j.helpers.DateLayout
 
 trait Logging {
-  protected val logger = Logger.getLogger(getClass.getSimpleName.split("\\$").last)
+  def logger = Logging.logger
+}
+
+object Logging {
+  val logger = Logger.getLogger("Logging")
 
-  private[core] val logLayout = new DateLayout() {
+  val logLayout = new DateLayout() {
     val ignoresThrowable = false
     def format(event: org.apache.log4j.spi.LoggingEvent): String = {
       val calendar: Calendar = Calendar.getInstance
@@ -18,10 +22,13 @@ trait Logging {
       val formattedDate: String = formatter.format(calendar.getTime)
       var logLevel = event.getLevel.toString
       while (logLevel.size < 6) logLevel += " "
-      logLevel + " [" + formattedDate + "] [" + event.getLoggerName + "] " + event.getMessage + "\n"
+      val className = event.getLocationInformation.getClassName.split("\\.").last.split("\\$").head
+      logLevel + " [" + formattedDate + "] [" + className + "] " + event.getMessage + "\n"
     }
   }
-  private[core] val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
+
+  val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
+
   logger.setLevel(org.apache.log4j.Level.INFO)
-  logger.addAppender(stderrAppender)
-}
+  logger.addAppender(Logging.stderrAppender)
+}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 97bc2e5e6b1d244ec8ee1b0fc3d96ad028421192..81f81f26aafed8ba2126217acec768232077084d 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -1,6 +1,6 @@
 package nl.lumc.sasc.biopet.core
 
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
 
 trait MultiSampleQScript extends BiopetQScript {
   type LibraryOutput <: AbstractLibraryOutput
@@ -20,7 +20,7 @@ trait MultiSampleQScript extends BiopetQScript {
   final def runSamplesJobs() {
     samplesConfig = config("samples")
     if (samplesConfig == null) samplesConfig = Map()
-    if (globalConfig.contains("samples")) for ((key, value) <- samplesConfig) {
+    if (Config.global.contains("samples")) for ((key, value) <- samplesConfig) {
       var sample = Configurable.any2map(value)
       if (!sample.contains("ID")) sample += ("ID" -> key)
       if (sample("ID") == key) {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
index 0a5dc8428cec541fd6cf1b967893e7266bcb1575..6cbef5b674f11d7bdffd7e5e9f766214932a8ba2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
@@ -9,10 +9,10 @@ trait ToolCommand extends MainCommand with Logging {
 
   abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
     opt[Unit]("log_nostderr") foreach { _ =>
-      logger.removeAppender(stderrAppender)
+      logger.removeAppender(Logging.stderrAppender)
     } text ("No output to stderr")
     opt[File]("log_file") foreach { x =>
-      logger.addAppender(new WriterAppender(logLayout, new java.io.PrintStream(x)))
+      logger.addAppender(new WriterAppender(Logging.logLayout, new java.io.PrintStream(x)))
     } text ("Log file") valueName ("<file>")
     opt[String]('l', "log_level") foreach { x =>
       x.toLowerCase match {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index 219374597ca3a780c35e7c8585e2a97ca53d6a1d..f6f8e0cf7ada60b11d50e8671b804350b54c5ad5 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -1,7 +1,7 @@
 package nl.lumc.sasc.biopet.core.config
 
 import java.io.File
-import org.broadinstitute.gatk.queue.util.Logging
+import nl.lumc.sasc.biopet.core.Logging
 import argonaut._, Argonaut._
 import scalaz._, Scalaz._
 
@@ -104,7 +104,9 @@ class Config(var map: Map[String, Any]) extends Logging {
   override def toString(): String = map.toString
 }
 
-object Config {
+object Config extends Logging {
+  val global = new Config
+
   def valueToMap(input: Any): Map[String, Any] = {
     input match {
       case m: Map[_, _] => return m.asInstanceOf[Map[String, Any]]
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index 62cd27d6bc12f12283a43e065441306c6eecc178..7f6f6cb8e3e958a3ad121411dbe133603f45fdb4 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -6,16 +6,16 @@ import scala.language.implicitConversions
 
 trait Configurable extends Logging {
   val root: Configurable
-  val globalConfig: Config = if (root != null) root.globalConfig else new Config()
+  //val globalConfig: Config = if (root != null) root.globalConfig else new Config()
   def configPath: List[String] = if (root != null) root.configFullPath else List()
   protected lazy val configName = getClass.getSimpleName.toLowerCase
   protected lazy val configFullPath = configName :: configPath
   var defaults: scala.collection.mutable.Map[String, Any] = if (root != null) scala.collection.mutable.Map(root.defaults.toArray: _*)
   else scala.collection.mutable.Map()
 
-  val config = new ConfigFuntions
+  val config = new ConfigFunctions
 
-  protected class ConfigFuntions {
+  protected class ConfigFunctions {
     def apply(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar: Boolean = true): ConfigValue = {
       val m = if (submodule != null) submodule else configName
       val p = if (submodule != null) configName :: configPath else configPath
@@ -29,15 +29,15 @@ trait Configurable extends Logging {
           throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
         } else return null
       }
-      if (d == null) return globalConfig(m, p, key, freeVar)
-      else return globalConfig(m, p, key, d, freeVar)
+      if (d == null) return Config.global(m, p, key, freeVar)
+      else return Config.global(m, p, key, d, freeVar)
     }
 
     def contains(key: String, submodule: String = null, freeVar: Boolean = true) = {
       val m = if (submodule != null) submodule else configName
       val p = if (submodule != null) configName :: configPath else configPath
 
-      globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
+      Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
     }
   }
 
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index f9d1dd1467630060f9cb162511eddf9044fec8a3..00904552adbaa21985d96c5090e5c2f24eb629d2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -11,7 +11,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
     if (config.contains("scattercount")) scatterCount = config("scattercount")
     if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
     this.sample_ploidy = config("ploidy")
-    nct = config("threads", default = 3)
+    nct = config("threads", default = 1)
     bamOutput = config("bamOutput")
     memoryLimit = Option(nct.getOrElse(1) * 2)
     if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 96cc081492fd65b350d8f28b2e75e7d776779811..75105f1b200592926c1461b9722ad0a5a35b6a7c 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -10,7 +10,7 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
     if (config.contains("scattercount")) scatterCount = config("scattercount")
     if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
     this.sample_ploidy = config("ploidy")
-    nct = config("threads", default = 3)
+    nct = config("threads", default = 1)
     memoryLimit = Option(nct.getOrElse(1) * 2)
     if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
     if (config.contains("output_mode")) {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index fdb2493a6b48e05f3bca9d7f79760887016a81b6..f30960a2b0932e59dc6cf3ba3881cf5291fda62d 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -26,7 +26,6 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
   var wholeGenome = false
 
   def init() {
-    for (file <- configfiles) globalConfig.loadConfigFile(file)
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
     if (config.contains("target_bed")) {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index b0366e5f5bcf0036ed5e64c8ee5c7f3dcb87c8ef..a120a1374f82b2b748571c15e9b40750730192a9 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -18,10 +18,10 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   var input_R2: File = _
 
   @Argument(doc = "Skip Trim fastq files", shortName = "skiptrim", required = false)
-  var skipTrim: Boolean = false
+  var skipTrim: Boolean = config("skiptrim", default = false)
 
   @Argument(doc = "Skip Clip fastq files", shortName = "skipclip", required = false)
-  var skipClip: Boolean = false
+  var skipClip: Boolean = config("skipclip", default = false)
 
   @Argument(doc = "Sample name", shortName = "sample", required = true)
   var sampleName: String = _
@@ -43,9 +43,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   val summary = new FlexiprepSummary(this)
 
   def init() {
-    for (file <- configfiles) globalConfig.loadConfigFile(file)
-    if (!skipTrim) skipTrim = config("skiptrim", default = false)
-    if (!skipClip) skipClip = config("skipclip", default = false)
     if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
     if (sampleName == null) throw new IllegalStateException("Missing Sample name on flexiprep module")
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
index d26f27e9c07fbc2fb5c6df5117fb89c6f7c8b470..23740daf48fd2f7c4e04e17d7aafe01b24950781 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
@@ -18,18 +18,15 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
   @Input(doc = "Gvcf files", shortName = "I", required = false)
   var gvcfFiles: List[File] = Nil
 
-  @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference")
 
   @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
-  var dbsnp: File = _
+  var dbsnp: File = config("dbsnp")
 
   def init() {
     if (config.contains("gvcffiles")) for (file <- config("gvcffiles").getList) {
       gvcfFiles ::= file.toString
     }
-    if (reference == null) reference = config("reference")
-    if (dbsnp == null) dbsnp = config("dbsnp")
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
   }
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
index 37adabdc507c686256fbd732d39e72558e079d0b..5ed4f062982c6b64516d651b50c9008953f4b7a2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
@@ -13,10 +13,10 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
   var inputGvcfs: List[File] = Nil
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference")
 
   @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
-  var dbsnp: File = _
+  var dbsnp: File = config("dbsnp")
 
   @Argument(doc = "OutputName", required = false)
   var outputName: String = "genotype"
@@ -28,8 +28,6 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
   var samples: List[String] = Nil
 
   def init() {
-    if (reference == null) reference = config("reference")
-    if (dbsnp == null) dbsnp = config("dbsnp")
     if (outputFile == null) outputFile = outputDir + outputName + ".vcf.gz"
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 9af84cbbba2212472450b94aefdbe49bc457fd43..c5bb656d039e5bb2b9b19792d03f7a7d2cfaa75c 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -27,17 +27,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   var mergeGvcfs: Boolean = false
 
   @Argument(doc = "Joint variantcalling", shortName = "jointVariantCalling", required = false)
-  var jointVariantcalling = false
+  var jointVariantcalling: Boolean = config("joint_variantcalling", default = false)
 
   @Argument(doc = "Joint genotyping", shortName = "jointGenotyping", required = false)
-  var jointGenotyping = false
+  var jointGenotyping: Boolean = config("joint_genotyping", default = false)
 
-  var singleSampleCalling = true
-  var reference: File = _
-  var dbsnp: File = _
+  var singleSampleCalling = config("single_sample_calling", default = true)
+  var reference: File = config("reference", required = true)
+  var dbsnp: File = config("dbsnp")
   var gvcfFiles: List[File] = Nil
   var finalBamFiles: List[File] = Nil
-  var useAllelesOption: Boolean = _
+  var useAllelesOption: Boolean = config("use_alleles_option", default = false)
 
   class LibraryOutput extends AbstractLibraryOutput {
     var mappedBamFile: File = _
@@ -49,15 +49,9 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   }
 
   def init() {
-    useAllelesOption = config("use_alleles_option", default = false)
-    reference = config("reference", required = true)
-    dbsnp = config("dbsnp")
     if (config.contains("target_bed")) {
       defaults ++= Map("gatk" -> Map(("intervals" -> config("target_bed").getStringList)))
     }
-    jointVariantcalling = config("joint_variantcalling", default = false)
-    jointGenotyping = config("joint_genotyping", default = false)
-    singleSampleCalling = config("single_sample_calling", default = true)
     if (config.contains("gvcfFiles"))
       for (file <- config("gvcfFiles").getList)
         gvcfFiles :+= file.toString
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index e4899798f13141998c9f8f81fe4988c31f4f9660..b016e17dc071f4a7704334bc5f81882263e2ceba 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File
-import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter }
+import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, MergeAlleles }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper }
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
@@ -24,10 +24,10 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   var rawVcfInput: File = _
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference", required = true)
 
   @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
-  var dbsnp: File = _
+  var dbsnp: File = config("dbsnp")
 
   @Argument(doc = "OutputName", required = false)
   var outputName: String = _
@@ -35,21 +35,14 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   @Argument(doc = "Sample name", required = false)
   var sampleID: String = _
 
-  var preProcesBams: Option[Boolean] = None
+  var preProcesBams: Option[Boolean] = config("pre_proces_bams", default = true)
   var variantcalling: Boolean = true
-  var doublePreProces: Option[Boolean] = None
-  var useHaplotypecaller: Option[Boolean] = None
-  var useUnifiedGenotyper: Option[Boolean] = None
-  var useAllelesOption: Option[Boolean] = None
+  var doublePreProces: Option[Boolean] = config("double_pre_proces", default = true)
+  var useHaplotypecaller: Option[Boolean] = config("use_haplotypecaller", default = true)
+  var useUnifiedGenotyper: Option[Boolean] = config("use_unifiedgenotyper", default = false)
+  var useAllelesOption: Option[Boolean] = config("use_alleles_option", default = false)
 
   def init() {
-    if (useAllelesOption == None) useAllelesOption = config("use_alleles_option", default = false)
-    if (preProcesBams == None) preProcesBams = config("pre_proces_bams", default = true)
-    if (doublePreProces == None) doublePreProces = config("double_pre_proces", default = true)
-    if (useHaplotypecaller == None) useHaplotypecaller = config("use_haplotypecaller", default = true)
-    if (useUnifiedGenotyper == None) useUnifiedGenotyper = config("use_unifiedgenotyper", default = false)
-    if (reference == null) reference = config("reference", required = true)
-    if (dbsnp == null) dbsnp = config("dbsnp")
     if (outputName == null && sampleID != null) outputName = sampleID
     else if (outputName == null) outputName = "noname"
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
@@ -142,26 +135,14 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
 
       if (useAllelesOption.get) {
-        val tempFile = if (mergeList.toList.size > 1) {
-          val allelesTemp = CombineVariants(this, mergeList.toList, outputDir + outputName + ".alleles_temp.vcf.gz")
-          allelesTemp.genotypemergeoption = org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.GenotypeMergeType.UNSORTED
-          add(allelesTemp, isIntermediate = true)
-          allelesTemp.out
-        } else mergeList.toList.head
-
-        val alleleOnly = new CommandLineFunction {
-          @Input val input: File = tempFile
-          @Output val output: File = outputDir + "raw.allele_only.vcf.gz"
-          @Output val outputindex: File = outputDir + "raw.allele__temp_only.vcf.gz.tbi"
-          def commandLine = "zcat " + input + " | cut -f1,2,3,4,5,6,7,8 | bgzip -c > " + output + " && tabix -pvcf " + output
-        }
-        add(alleleOnly, isIntermediate = true)
+        val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz")
+        add(mergeAlleles, isIntermediate = true)
 
         if (useHaplotypecaller.get) {
           val hcAlleles = new HaplotypeCaller(this)
           hcAlleles.input_file = scriptOutput.bamFiles
           hcAlleles.out = outputDir + outputName + ".hc.allele.vcf.gz"
-          hcAlleles.alleles = alleleOnly.output
+          hcAlleles.alleles = mergeAlleles.output
           hcAlleles.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
           add(hcAlleles)
           scriptOutput.hcAlleleVcf = hcAlleles.out
@@ -172,7 +153,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
           val ugAlleles = new UnifiedGenotyper(this)
           ugAlleles.input_file = scriptOutput.bamFiles
           ugAlleles.out = outputDir + outputName + ".ug.allele.vcf.gz"
-          ugAlleles.alleles = alleleOnly.output
+          ugAlleles.alleles = mergeAlleles.output
           ugAlleles.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
           add(ugAlleles)
           scriptOutput.ugAlleleVcf = ugAlleles.out
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
index 067012e443ee81958910e07fa0eb8c8361293bd8..2669dc2b38ce5751f14208e41ca64714f1489759 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
@@ -16,7 +16,7 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
   var vcfFiles: List[File] = _
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference")
 
   @Argument(doc = "Target bed", shortName = "targetBed", required = false)
   var targetBed: List[File] = Nil
@@ -29,7 +29,6 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
   def generalSampleDir = outputDir + "samples/"
 
   def init() {
-    if (reference == null) reference = config("reference")
     if (config.contains("target_bed"))
       for (bed <- config("target_bed").getList)
         targetBed :+= bed.toString
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index fb159e9b8b05b83e5f08fa0664a6ae9ecdd41b7a..d254b51d7baabafbbb7cc0302f8abb5c25a660b2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -69,7 +69,7 @@ class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
   var cExonBase: Boolean = _
 
   def init() {
-    for (file <- configfiles) globalConfig.loadConfigFile(file)
+
   }
 
   def biopetScript() {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index ad1406f566dab1c061e7cb52f7feae8e9c260df9..68194858396b0e34b35ed85cc04d31c369d39e03 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -36,13 +36,13 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
   var skipMetrics: Boolean = false
 
   @Argument(doc = "Aligner", shortName = "ALN", required = false)
-  var aligner: String = _
+  var aligner: String = config("aligner", default = "bwa")
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = _
+  var reference: File = config("reference")
 
   @Argument(doc = "Chunking", shortName = "chunking", required = false)
-  var chunking: Boolean = false
+  var chunking: Boolean = config("chunking", false)
 
   @ClassType(classOf[Int])
   @Argument(doc = "Number of chunks, when not defined pipeline will automatic calculate number of chunks", shortName = "numberChunks", required = false)
@@ -50,62 +50,48 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
 
   // Readgroup items
   @Argument(doc = "Readgroup ID", shortName = "RGID", required = false)
-  var RGID: String = _
+  var RGID: String = config("RGID")
 
   @Argument(doc = "Readgroup Library", shortName = "RGLB", required = false)
-  var RGLB: String = _
+  var RGLB: String = config("RGLB")
 
   @Argument(doc = "Readgroup Platform", shortName = "RGPL", required = false)
-  var RGPL: String = _
+  var RGPL: String = config("RGPL", default = "illumina")
 
   @Argument(doc = "Readgroup platform unit", shortName = "RGPU", required = false)
-  var RGPU: String = _
+  var RGPU: String = config("RGPU", default = "na")
 
   @Argument(doc = "Readgroup sample", shortName = "RGSM", required = false)
-  var RGSM: String = _
+  var RGSM: String = config("RGSM")
 
   @Argument(doc = "Readgroup sequencing center", shortName = "RGCN", required = false)
-  var RGCN: String = _
+  var RGCN: String = config("RGCN")
 
   @Argument(doc = "Readgroup description", shortName = "RGDS", required = false)
-  var RGDS: String = _
+  var RGDS: String = config("RGDS")
 
   @Argument(doc = "Readgroup sequencing date", shortName = "RGDT", required = false)
   var RGDT: Date = _
 
   @Argument(doc = "Readgroup predicted insert size", shortName = "RGPI", required = false)
-  var RGPI: Int = _
+  var RGPI: Int = config("RGPI")
 
   var paired: Boolean = false
-  var defaultAligner = "bwa"
   val flexiprep = new Flexiprep(this)
 
   def init() {
-    for (file <- configfiles) globalConfig.loadConfigFile(file)
-    if (aligner == null) aligner = config("aligner", default = defaultAligner)
-    if (reference == null) reference = config("reference")
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
     if (input_R1 == null) throw new IllegalStateException("Missing FastQ R1 on mapping module")
     paired = (input_R2 != null)
 
-    if (RGLB == null && config.contains("RGLB")) RGLB = config("RGLB")
-    else if (RGLB == null) throw new IllegalStateException("Missing Readgroup library on mapping module")
-    if (RGSM == null && config.contains("RGSM")) RGSM = config("RGSM")
-    else if (RGLB == null) throw new IllegalStateException("Missing Readgroup sample on mapping module")
-    if (RGID == null && config.contains("RGID")) RGID = config("RGID")
-    else if (RGID == null && RGSM != null && RGLB != null) RGID = RGSM + "-" + RGLB
+    if (RGLB == null) throw new IllegalStateException("Missing Readgroup library on mapping module")
+    if (RGLB == null) throw new IllegalStateException("Missing Readgroup sample on mapping module")
+    if (RGID == null && RGSM != null && RGLB != null) RGID = RGSM + "-" + RGLB
     else if (RGID == null) throw new IllegalStateException("Missing Readgroup ID on mapping module")
 
-    if (RGPL == null) RGPL = config("RGPL", "illumina")
-    if (RGPU == null) RGPU = config("RGPU", "na")
-    if (RGCN == null && config.contains("RGCN")) RGCN = config("RGCN")
-    if (RGDS == null && config.contains("RGDS")) RGDS = config("RGDS")
-
     if (outputName == null) outputName = RGID
 
-    if (!chunking && numberChunks.isDefined) chunking = true
-    if (!chunking) chunking = config("chunking", false)
     if (chunking) {
       if (numberChunks.isEmpty) {
         if (config.contains("numberchunks")) numberChunks = config("numberchunks", default = None)
@@ -311,10 +297,6 @@ object Mapping extends PipelineCommand {
     val mapping = new Mapping(root)
 
     logger.debug("Mapping runconfig: " + runConfig)
-    var inputType = ""
-    if (runConfig.contains("inputtype")) inputType = runConfig("inputtype").toString
-    else inputType = root.config("inputtype", "dna").getString
-    if (inputType == "rna") mapping.defaultAligner = "star-2pass"
     if (runConfig.contains("R1")) mapping.input_R1 = new File(runConfig("R1").toString)
     if (runConfig.contains("R2")) mapping.input_R2 = new File(runConfig("R2").toString)
     mapping.paired = (mapping.input_R2 != null)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index 937b84261a20935025aeb79c4f555a7fdfb6827b..7a826e9bb6412d053ff240b1c7e5bc08e9258388 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -20,15 +20,15 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
   def this() = this(null)
 
   @Input(doc = "countBed", required = false)
-  var countBed: File = _
+  var countBed: File = config("count_bed")
 
   @Input(doc = "squishedCountBed, by suppling this file the auto squish job will be skipped", required = false)
-  var squishedCountBed: File = _
+  var squishedCountBed: File = config("squished_count_bed")
 
   @Input(doc = "Transcriptome, used for generation of tag library", required = false)
-  var transcriptome: File = _
+  var transcriptome: File = config("transcriptome")
 
-  var tagsLibrary: File = _
+  var tagsLibrary: File = config("tags_library")
 
   defaults ++= Map("bowtie" -> Map(
     "m" -> 1,
@@ -50,10 +50,6 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
 
   def init() {
     if (!outputDir.endsWith("/")) outputDir += "/"
-    if (countBed == null) countBed = config("count_bed")
-    if (squishedCountBed == null) squishedCountBed = config("squished_count_bed")
-    if (tagsLibrary == null) tagsLibrary = config("tags_library")
-    if (transcriptome == null) transcriptome = config("transcriptome")
     if (transcriptome == null && tagsLibrary == null)
       throw new IllegalStateException("No transcriptome or taglib found")
     if (countBed == null && squishedCountBed == null)
@@ -140,7 +136,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       val mapping = new Mapping(this)
       mapping.skipFlexiprep = true
       mapping.skipMarkduplicates = true
-      mapping.defaultAligner = "bowtie"
+      mapping.aligner = config("aligner", default = "bowtie")
       mapping.input_R1 = prefixFastq.output
       mapping.RGLB = runConfig("ID").toString
       mapping.RGSM = sampleConfig("ID").toString
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 10aef464b610c43571398d6285d3ddd7bc9c5b3c..a428eb693211f1787c72990a7f68ef8df225cc95 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.queue.engine.JobRunInfo
 class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
   def this() = this(null)
 
-  var reference: File = _
+  var reference: File = config("reference", required = true)
   var finalBamFiles: List[File] = Nil
 
   class LibraryOutput extends AbstractLibraryOutput {
@@ -34,8 +34,6 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
   }
 
   override def init() {
-    for (file <- configfiles) globalConfig.loadConfigFile(file)
-    reference = config("reference", required = true)
     if (outputDir == null)
       throw new IllegalStateException("Output directory is not specified in the config / argument")
     else if (!outputDir.endsWith("/"))
@@ -124,7 +122,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
     if (runConfig.contains("R1")) {
       val mapping = new Mapping(this)
 
-      mapping.defaultAligner = "stampy"
+      mapping.aligner = config("aligner", default = "stampy")
       mapping.skipFlexiprep = false
       mapping.skipMarkduplicates = true // we do the dedup marking using Sambamba
 
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
new file mode 100644
index 0000000000000000000000000000000000000000..454f9a41fb27ece87ae193ed64185acd5ea02b69
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -0,0 +1,134 @@
+package nl.lumc.sasc.biopet.tools
+
+import htsjdk.samtools.reference.FastaSequenceFile
+import htsjdk.variant.variantcontext.Allele
+import htsjdk.variant.variantcontext.VariantContext
+import htsjdk.variant.variantcontext.VariantContextBuilder
+import htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
+import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
+import htsjdk.variant.vcf.VCFFileReader
+import htsjdk.variant.vcf.VCFHeader
+import java.io.File
+import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.core.ToolCommand
+import scala.collection.SortedMap
+import scala.collection.mutable.{ Map, Set }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import scala.collection.JavaConversions._
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction {
+  javaMainClass = getClass.getName
+
+  @Input(doc = "Input vcf files", shortName = "input", required = true)
+  var input: List[File] = Nil
+
+  @Output(doc = "Output vcf file", shortName = "output", required = true)
+  var output: File = _
+
+  @Output(doc = "Output vcf file index", shortName = "output", required = true)
+  private var outputIndex: File = _
+
+  var reference: File = config("reference")
+
+  override val defaultVmem = "8G"
+  memoryLimit = Option(4)
+
+  override def afterGraph {
+    super.afterGraph
+    if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
+    if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
+  }
+
+  override def commandLine = super.commandLine +
+    repeat("-I", input) +
+    required("-o", output) +
+    required("-R", reference)
+}
+
+object MergeAlleles extends ToolCommand {
+  def apply(root: Configurable, input: List[File], output: File): MergeAlleles = {
+    val mergeAlleles = new MergeAlleles(root)
+    mergeAlleles.input = input
+    mergeAlleles.output = output
+    return mergeAlleles
+  }
+
+  case class Args(inputFiles: List[File] = Nil, outputFile: File = null, reference: File = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('I', "inputVcf") minOccurs (2) required () unbounded () valueName ("<file>") action { (x, c) =>
+      c.copy(inputFiles = x :: c.inputFiles)
+    }
+    opt[File]('o', "outputVcf") required () unbounded () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+      c.copy(outputFile = x)
+    }
+    opt[File]('R', "reference") required () unbounded () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+      c.copy(reference = x)
+    }
+  }
+
+  private val chunkSize = 50000
+
+  /**
+   * @param args the command line arguments
+   */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+    val readers = commandArgs.inputFiles.map(new VCFFileReader(_, true))
+    val referenceFile = new FastaSequenceFile(commandArgs.reference, true)
+    val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().setOutputFile(commandArgs.outputFile).build)
+    val header = new VCFHeader
+    val referenceDict = referenceFile.getSequenceDictionary
+    header.setSequenceDictionary(referenceDict)
+    writer.writeHeader(header)
+
+    for (chr <- referenceDict.getSequences; chunk <- (0 to (chr.getSequenceLength / chunkSize))) {
+      val output: Map[Int, List[VariantContext]] = Map()
+
+      val chrName = chr.getSequenceName
+      val begin = chunk * chunkSize + 1
+      val end = {
+        val e = (chunk + 1) * chunkSize
+        if (e > chr.getSequenceLength) chr.getSequenceLength else e
+      }
+
+      for (reader <- readers; variant <- reader.query(chrName, begin, end)) {
+        val start = variant.getStart
+        if (output.contains(start)) output += variant.getStart -> (variant :: output(start))
+        else output += variant.getStart -> List(variant)
+      }
+
+      for ((k, v) <- SortedMap(output.toSeq: _*)) {
+        writer.add(mergeAlleles(v))
+      }
+    }
+    writer.close
+    readers.foreach(_.close)
+  }
+
+  def mergeAlleles(records: List[VariantContext]): VariantContext = {
+    val longestRef = {
+      var l: Array[Byte] = Array()
+      for (a <- records.map(_.getReference.getBases) if (a.length > l.size)) l = a
+      Allele.create(l, true)
+    }
+    val alleles: Set[Allele] = Set()
+    val builder = new VariantContextBuilder
+    builder.chr(records.head.getChr)
+    builder.start(records.head.getStart)
+
+    for (record <- records) {
+      if (record.getReference == longestRef) alleles ++= record.getAlternateAlleles
+      else {
+        val suffix = longestRef.getBaseString.stripPrefix(record.getReference.getBaseString)
+        for (r <- record.getAlternateAlleles) alleles += Allele.create(r.getBaseString + suffix)
+      }
+    }
+    builder.alleles(longestRef :: alleles.toList)
+    builder.computeEndFromAlleles(longestRef :: alleles.toList, records.head.getStart)
+    builder.make
+  }
+}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index 9c364cf62da705beaa94cb682b59a33c7e3329ef..3d11e5452d63b6c87a472ec22ee05454a66d7496 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -74,16 +74,16 @@ object MpileupToVcf extends ToolCommand {
     opt[String]('s', "sample") required () action { (x, c) =>
       c.copy(sample = x)
     }
-    opt[Int]("minDP") required () action { (x, c) =>
+    opt[Int]("minDP") action { (x, c) =>
       c.copy(minDP = x)
     }
-    opt[Int]("minAP") required () action { (x, c) =>
+    opt[Int]("minAP") action { (x, c) =>
       c.copy(minAP = x)
     }
-    opt[Double]("homoFraction") required () action { (x, c) =>
+    opt[Double]("homoFraction") action { (x, c) =>
       c.copy(homoFraction = x)
     }
-    opt[Int]("ploidy") required () action { (x, c) =>
+    opt[Int]("ploidy") action { (x, c) =>
       c.copy(ploidy = x)
     }
   }