diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
index 749ac33a2176ac7b2d6e78e0ca2bb33c85c61877..0e8e31ba48e60d2960a91246304be0e673c8055f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.core
import java.io.{ PrintWriter, StringWriter }
import nl.lumc.sasc.biopet.core.BiopetExecutable._
+import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.{ FullVersion, LastCommitHash }
import org.apache.log4j.Logger
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 8bcb354588c52400cc2c6677839e5970149be191..24bed211de0364f1494b590415a10df086573a99 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
+import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index 612a3753d3cf6d49a86e7c577bf51da0c5880948..90857d202d977ed76d3317ea6671003d2869cf6a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -19,6 +19,7 @@ import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
+import nl.lumc.sasc.biopet.utils.Logging
import org.apache.log4j.{ PatternLayout, WriterAppender }
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
index 68451bc26139618b987552ba05766aa512497ec0..091da17d6d53ab7862c43a94b35554af03d3770c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.core
import nl.lumc.sasc.biopet.FullVersion
+import nl.lumc.sasc.biopet.utils.Logging
/**
* Trait for biopet tools, sets some default args
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index 10099c57983b7f0f5af4cf1070b1ed7d6753ac69..e7c86664b90c8d66bd498590ba3f7cc215f2fa7b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -16,9 +16,7 @@
package nl.lumc.sasc.biopet.core.config
import java.io.{ File, PrintWriter }
-
-import nl.lumc.sasc.biopet.core.Logging
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{Logging, ConfigUtils}
import nl.lumc.sasc.biopet.utils.ConfigUtils._
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
index e52bb1f5a9074f779f74d643cc3238ed22443d38..21970b6ea3c78e8a28d35af0cd9ad82a906d7a39 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
@@ -18,8 +18,8 @@ package nl.lumc.sasc.biopet.core.report
import java.io._
import nl.lumc.sasc.biopet.core.summary.Summary
-import nl.lumc.sasc.biopet.core.{ Logging, ToolCommand, ToolCommandFuntion }
-import nl.lumc.sasc.biopet.utils.IoUtils
+import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.utils.{Logging, IoUtils}
import org.broadinstitute.gatk.utils.commandline.Input
import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
import scala.collection.mutable
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
index 2092ea7324cb62997debf195189169744de26281..a2c4b8c2507e95d83618fc54e3f238ccfa009769 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
@@ -50,7 +50,7 @@ import java.util
import java.util.ResourceBundle
import nl.lumc.sasc.biopet.FullVersion
-import nl.lumc.sasc.biopet.core.Logging
+import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.queue.engine.{ QGraph, QGraphSettings }
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging, ScalaCompoundArgumentTypeDescriptor, ClassFieldCache }
import org.broadinstitute.gatk.queue.{ QCommandPlugin, QScript, QScriptManager }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index d5f3b2078b706a269e6ef4754ce35db447b39841..dbfedea6ae60373c6ffdfdec12e0bacb89ceecf5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Logging }
-import nl.lumc.sasc.biopet.utils.tryToParseNumber
+import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.utils.{Logging, tryToParseNumber}
import org.broadinstitute.gatk.utils.commandline.Argument
import scala.io.Source
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 6c1795f48acaecac0dabb01c75238bc1f8ffca13..bb324e57280346b5b1ee1f745645d18846ca75fb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -19,7 +19,8 @@ import java.io.File
import argonaut.Argonaut._
import argonaut._
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, Logging }
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.core.{ BiopetQScript }
import nl.lumc.sasc.biopet.core.config.ConfigValue
import org.yaml.snakeyaml.Yaml
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
index 4566cd4f1b26f08f2af84e31735b6514dfd10d6a..3189486132d1d1775eb9598462c00c8f4eda736e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet.utils
import org.apache.log4j.Logger
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
index c03c4bccc9e22b0b103e032910ea4338fdc3ed42..56b2f303b0a7161879ea9ae01eaf3ba1cc0b86f7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
@@ -9,7 +9,7 @@ import scala.collection.JavaConversions._
import scala.collection.mutable
import scala.collection.mutable.ListBuffer
import scala.io.Source
-import nl.lumc.sasc.biopet.core.Logging
+import nl.lumc.sasc.biopet.utils.Logging
/**
* Created by pjvan_thof on 8/20/15.
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala