Added protected artifact for gatk pipelines

protected/biopet-gatk-pipelines/.gitignore

+/target/
\ No newline at end of file

protected/biopet-gatk-pipelines/pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>nl.lumc.sasc</groupId>
+    <artifactId>BiopetGatkPipelines</artifactId>
+    <version>0.2.0-DEV</version>
+    <packaging>jar</packaging>
+    
+    <inceptionYear>2014</inceptionYear>
+    <name>BiopetGatkPipelines</name>
+    <url>http://maven.apache.org</url>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <sting.unpack.phase>prepare-package</sting.unpack.phase>
+        <sting.shade.phase>package</sting.shade.phase>
+        <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutable</app.main.class>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>0.2.0-DEV</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetGatkExtensions</artifactId>
+            <version>0.2.0-DEV</version>
+        </dependency>
+    </dependencies>
+    <build>
+        <resources>
+            <resource>
+                <directory>src/main/resources</directory>
+                <includes>
+                    <include>**/*</include>
+                </includes>
+            </resource>
+        </resources>
+        <plugins>
+            <plugin>
+                <groupId>org.scala-tools</groupId>
+                <artifactId>maven-scala-plugin</artifactId>
+                <version>2.15.2</version>
+                <executions>
+                    <execution>
+                        <id>scala-compile</id>
+                        <goals>
+                            <goal>compile</goal>
+                            <goal>testCompile</goal>
+                        </goals>
+                        <configuration>
+                            <args>
+                                <arg>-dependencyfile</arg>
+                                <arg>${project.build.directory}/.scala_dependencies</arg>
+                                <arg>-deprecation</arg>
+                                <arg>-feature</arg>
+                            </args>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>2.5</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>2.3.2</version>
+                <configuration>
+                    <showDeprecation>true</showDeprecation>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

+package nl.lumc.sasc.biopet.pipelines.gatk
+
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+import scala.util.Random
+
+class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "Sample gvcf file")
+  var sampleGvcf: File = _
+
+  @Argument(doc = "SampleName", required = true)
+  var sampleName: String = _
+
+  @Input(doc = "Gvcf files", shortName = "I", required = false)
+  var gvcfFiles: List[File] = Nil
+
+  var reference: File = config("reference")
+
+  @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
+  var dbsnp: File = config("dbsnp")
+
+  def init() {
+    if (config.contains("gvcffiles")) for (file <- config("gvcffiles").asList) {
+      gvcfFiles ::= file.toString
+    }
+    if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
+    else if (!outputDir.endsWith("/")) outputDir += "/"
+  }
+
+  def biopetScript() {
+    var todoGvcfs = gvcfFiles
+    var gvcfPool: List[File] = Nil
+    addGenotypingPipeline(gvcfPool)
+
+    while (todoGvcfs.size > 0) {
+      val index = Random.nextInt(todoGvcfs.size)
+      gvcfPool ::= todoGvcfs(index)
+      addGenotypingPipeline(gvcfPool)
+      todoGvcfs = todoGvcfs.filter(b => b != todoGvcfs(index))
+    }
+  }
+
+  def addGenotypingPipeline(gvcfPool: List[File]) {
+    val gatkGenotyping = new GatkGenotyping(this)
+    gatkGenotyping.inputGvcfs = sampleGvcf :: gvcfPool
+    gatkGenotyping.samples :+= sampleName
+    gatkGenotyping.outputDir = outputDir + "samples_" + gvcfPool.size + "/"
+    gatkGenotyping.init
+    gatkGenotyping.biopetScript
+    addAll(gatkGenotyping.functions)
+  }
+}
+
+object GatkBenchmarkGenotyping extends PipelineCommand

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

+package nl.lumc.sasc.biopet.pipelines.gatk
+
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.gatk.{ GenotypeGVCFs, SelectVariants }
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+
+class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "Gvcf files", shortName = "I")
+  var inputGvcfs: List[File] = Nil
+
+  @Argument(doc = "Reference", shortName = "R", required = false)
+  var reference: File = config("reference")
+
+  @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
+  var dbsnp: File = config("dbsnp")
+
+  @Argument(doc = "OutputName", required = false)
+  var outputName: String = "genotype"
+
+  @Output(doc = "OutputFile", shortName = "O", required = false)
+  var outputFile: File = _
+
+  @Argument(doc = "Samples", shortName = "sample", required = false)
+  var samples: List[String] = Nil
+
+  def init() {
+    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 += "/"
+  }
+
+  def biopetScript() {
+    addGenotypeGVCFs(inputGvcfs, outputFile)
+    if (!samples.isEmpty) {
+      if (samples.size > 1) addSelectVariants(outputFile, samples, outputDir + "samples/", "all")
+      for (sample <- samples) addSelectVariants(outputFile, List(sample), outputDir + "samples/", sample)
+    }
+  }
+
+  def addGenotypeGVCFs(gvcfFiles: List[File], outputFile: File): File = {
+    val genotypeGVCFs = GenotypeGVCFs(this, gvcfFiles, outputFile)
+    add(genotypeGVCFs)
+    return genotypeGVCFs.out
+  }
+
+  def addSelectVariants(inputFile: File, samples: List[String], outputDir: String, name: String) {
+    val selectVariants = SelectVariants(this, inputFile, outputDir + name + ".vcf.gz")
+    selectVariants.excludeNonVariants = true
+    for (sample <- samples) selectVariants.sample_name :+= sample
+    add(selectVariants)
+  }
+}
+
+object GatkGenotyping extends PipelineCommand

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

+package nl.lumc.sasc.biopet.pipelines.gatk
+
+import nl.lumc.sasc.biopet.core.MultiSampleQScript
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.config.Configurable
+import htsjdk.samtools.SamReaderFactory
+import scala.collection.JavaConversions._
+import java.io.File
+import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
+import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
+import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
+import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
+import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.utils.commandline.{ Argument }
+
+class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScript {
+  def this() = this(null)
+
+  @Argument(doc = "Only Sample", shortName = "sample", required = false)
+  val onlySample: List[String] = Nil
+
+  @Argument(doc = "Skip Genotyping step", shortName = "skipgenotyping", required = false)
+  var skipGenotyping: Boolean = false
+
+  @Argument(doc = "Merge gvcfs", shortName = "mergegvcfs", required = false)
+  var mergeGvcfs: Boolean = false
+
+  @Argument(doc = "Joint variantcalling", shortName = "jointVariantCalling", required = false)
+  var jointVariantcalling: Boolean = config("joint_variantcalling", default = false)
+
+  @Argument(doc = "Joint genotyping", shortName = "jointGenotyping", required = false)
+  var jointGenotyping: Boolean = config("joint_genotyping", default = false)
+
+  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 = config("use_alleles_option", default = false)
+
+  class LibraryOutput extends AbstractLibraryOutput {
+    var mappedBamFile: File = _
+    var variantcalling: GatkVariantcalling.ScriptOutput = _
+  }
+
+  class SampleOutput extends AbstractSampleOutput {
+    var variantcalling: GatkVariantcalling.ScriptOutput = _
+  }
+
+  def init() {
+    if (config.contains("target_bed")) {
+      defaults ++= Map("gatk" -> Map(("intervals" -> config("target_bed").asStringList)))
+    }
+    if (config.contains("gvcfFiles"))
+      for (file <- config("gvcfFiles").asList)
+        gvcfFiles :+= file.toString
+    if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
+    else if (!outputDir.endsWith("/")) outputDir += "/"
+  }
+
+  val multisampleVariantcalling = new GatkVariantcalling(this) {
+    override protected lazy val configName = "gatkvariantcalling"
+    override def configPath: List[String] = "multisample" :: super.configPath
+  }
+
+  def biopetScript() {
+    if (onlySample.isEmpty) {
+      runSamplesJobs
+
+      //SampleWide jobs
+      if (mergeGvcfs && gvcfFiles.size > 0) {
+        val newFile = outputDir + "merged.gvcf.vcf.gz"
+        add(CombineGVCFs(this, gvcfFiles, newFile))
+        gvcfFiles = List(newFile)
+      }
+
+      if (!skipGenotyping && gvcfFiles.size > 0) {
+        if (jointGenotyping) {
+          val gatkGenotyping = new GatkGenotyping(this)
+          gatkGenotyping.inputGvcfs = gvcfFiles
+          gatkGenotyping.outputDir = outputDir + "genotyping/"
+          gatkGenotyping.init
+          gatkGenotyping.biopetScript
+          addAll(gatkGenotyping.functions)
+          var vcfFile = gatkGenotyping.outputFile
+        }
+      } else logger.warn("No gVCFs to genotype")
+
+      if (jointVariantcalling) {
+        val allBamfiles = for (
+          (sampleID, sampleOutput) <- samplesOutput;
+          file <- sampleOutput.variantcalling.bamFiles
+        ) yield file
+        val allRawVcfFiles = for ((sampleID, sampleOutput) <- samplesOutput) yield sampleOutput.variantcalling.rawFilterVcfFile
+
+        val gatkVariantcalling = new GatkVariantcalling(this) {
+          override protected lazy val configName = "gatkvariantcalling"
+          override def configPath: List[String] = "multisample" :: super.configPath
+        }
+
+        if (gatkVariantcalling.useMpileup) {
+          val cvRaw = CombineVariants(this, allRawVcfFiles.toList, outputDir + "variantcalling/multisample.raw.vcf.gz")
+          add(cvRaw)
+          gatkVariantcalling.rawVcfInput = cvRaw.out
+        }
+
+        multisampleVariantcalling.preProcesBams = false
+        multisampleVariantcalling.doublePreProces = false
+        multisampleVariantcalling.inputBams = allBamfiles.toList
+        multisampleVariantcalling.outputDir = outputDir + "variantcalling"
+        multisampleVariantcalling.outputName = "multisample"
+        multisampleVariantcalling.init
+        multisampleVariantcalling.biopetScript
+        addAll(multisampleVariantcalling.functions)
+
+        if (config("inputtype", default = "dna").asString != "rna" && config("recalibration", default = false).asBoolean) {
+          val recalibration = new GatkVariantRecalibration(this)
+          recalibration.inputVcf = multisampleVariantcalling.scriptOutput.finalVcfFile
+          recalibration.bamFiles = finalBamFiles
+          recalibration.outputDir = outputDir + "recalibration/"
+          recalibration.init
+          recalibration.biopetScript
+        }
+      }
+    } else for (sample <- onlySample) runSingleSampleJobs(sample)
+  }
+
+  // Called for each sample
+  def runSingleSampleJobs(sampleConfig: Map[String, Any]): SampleOutput = {
+    val sampleOutput = new SampleOutput
+    var libraryBamfiles: List[File] = List()
+    val sampleID: String = sampleConfig("ID").toString
+    sampleOutput.libraries = runLibraryJobs(sampleConfig)
+    val sampleDir = globalSampleDir + sampleID
+    for ((libraryID, libraryOutput) <- sampleOutput.libraries) {
+      libraryBamfiles ++= libraryOutput.variantcalling.bamFiles
+    }
+
+    if (libraryBamfiles.size > 0) {
+      finalBamFiles ++= libraryBamfiles
+      val gatkVariantcalling = new GatkVariantcalling(this)
+      gatkVariantcalling.inputBams = libraryBamfiles
+      gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
+      gatkVariantcalling.preProcesBams = false
+      if (!singleSampleCalling) {
+        gatkVariantcalling.useHaplotypecaller = false
+        gatkVariantcalling.useUnifiedGenotyper = false
+      }
+      gatkVariantcalling.sampleID = sampleID
+      gatkVariantcalling.init
+      gatkVariantcalling.biopetScript
+      addAll(gatkVariantcalling.functions)
+      sampleOutput.variantcalling = gatkVariantcalling.scriptOutput
+      gvcfFiles :+= gatkVariantcalling.scriptOutput.gvcfFile
+    } else logger.warn("No bamfiles for variant calling for sample: " + sampleID)
+    return sampleOutput
+  }
+
+  // Called for each run from a sample
+  def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): LibraryOutput = {
+    val libraryOutput = new LibraryOutput
+    val runID: String = runConfig("ID").toString
+    val sampleID: String = sampleConfig("ID").toString
+    val runDir: String = globalSampleDir + sampleID + "/run_" + runID + "/"
+    var inputType = ""
+    if (runConfig.contains("inputtype")) inputType = runConfig("inputtype").toString
+    else inputType = config("inputtype", default = "dna").toString
+    if (runConfig.contains("R1")) {
+      val mapping = Mapping.loadFromLibraryConfig(this, runConfig, sampleConfig, runDir)
+      addAll(mapping.functions) // Add functions of mapping to curent function pool
+      libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
+    } else if (runConfig.contains("bam")) {
+      var bamFile = new File(runConfig("bam").toString)
+      if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile)
+
+      if (config("bam_to_fastq", default = false).asBoolean) {
+        val samToFastq = SamToFastq(this, bamFile, runDir + sampleID + "-" + runID + ".R1.fastq",
+          runDir + sampleID + "-" + runID + ".R2.fastq")
+        add(samToFastq, isIntermediate = true)
+        val mapping = Mapping.loadFromLibraryConfig(this, runConfig, sampleConfig, runDir, startJobs = false)
+        mapping.input_R1 = samToFastq.fastqR1
+        mapping.input_R2 = samToFastq.fastqR2
+        mapping.init
+        mapping.biopetScript
+        addAll(mapping.functions) // Add functions of mapping to curent function pool
+        libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
+      } else {
+        var readGroupOke = true
+        val inputSam = SamReaderFactory.makeDefault.open(bamFile)
+        val header = inputSam.getFileHeader.getReadGroups
+        for (readGroup <- inputSam.getFileHeader.getReadGroups) {
+          if (readGroup.getSample != sampleID) logger.warn("Sample ID readgroup in bam file is not the same")
+          if (readGroup.getLibrary != runID) logger.warn("Library ID readgroup in bam file is not the same")
+          if (readGroup.getSample != sampleID || readGroup.getLibrary != runID) readGroupOke = false
+        }
+        inputSam.close
+
+        if (!readGroupOke) {
+          if (config("correct_readgroups", default = false)) {
+            logger.info("Correcting readgroups, file:" + bamFile)
+            val aorrg = AddOrReplaceReadGroups(this, bamFile, new File(runDir + sampleID + "-" + runID + ".bam"))
+            aorrg.RGID = sampleID + "-" + runID
+            aorrg.RGLB = runID
+            aorrg.RGSM = sampleID
+            if (runConfig.contains("PL")) aorrg.RGPL = runConfig("PL").toString
+            else aorrg.RGPL = "illumina"
+            if (runConfig.contains("PU")) aorrg.RGPU = runConfig("PU").toString
+            else aorrg.RGPU = "na"
+            if (runConfig.contains("CN")) aorrg.RGCN = runConfig("CN").toString
+            add(aorrg, isIntermediate = true)
+            bamFile = aorrg.output
+          } else throw new IllegalStateException("Readgroup sample and/or library of input bamfile is not correct, file: " + bamFile +
+            "\nPossible to set 'correct_readgroups' to true on config to automatic fix this")
+        }
+        addAll(BamMetrics(this, bamFile, runDir + "metrics/").functions)
+
+        libraryOutput.mappedBamFile = bamFile
+      }
+    } else logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig)
+
+    val gatkVariantcalling = new GatkVariantcalling(this)
+    gatkVariantcalling.inputBams = List(libraryOutput.mappedBamFile)
+    gatkVariantcalling.outputDir = runDir
+    gatkVariantcalling.variantcalling = config("library_variantcalling", default = false)
+    gatkVariantcalling.preProcesBams = true
+    gatkVariantcalling.sampleID = sampleID
+    gatkVariantcalling.init
+    gatkVariantcalling.biopetScript
+    addAll(gatkVariantcalling.functions)
+    libraryOutput.variantcalling = gatkVariantcalling.scriptOutput
+
+    return libraryOutput
+  }
+}
+
+object GatkPipeline extends PipelineCommand

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala

+package nl.lumc.sasc.biopet.pipelines.gatk
+
+import nl.lumc.sasc.biopet.core.BiopetQScript
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.gatk.ApplyRecalibration
+import nl.lumc.sasc.biopet.extensions.gatk.VariantAnnotator
+import nl.lumc.sasc.biopet.extensions.gatk.VariantRecalibrator
+import org.broadinstitute.gatk.queue.QScript
+
+class GatkVariantRecalibration(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "input vcf file", shortName = "I")
+  var inputVcf: File = _
+
+  @Input(doc = "input vcf file", shortName = "BAM", required = false)
+  var bamFiles: List[File] = Nil
+
+  @Output(doc = "output vcf file", shortName = "out")
+  var outputVcf: File = _
+
+  def init() {
+    if (inputVcf == null) throw new IllegalStateException("Missing Output directory on gatk module")
+    if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
+    else if (!outputDir.endsWith("/")) outputDir += "/"
+  }
+
+  def biopetScript() {
+    var vcfFile: File = if (!bamFiles.isEmpty) addVariantAnnotator(inputVcf, bamFiles, outputDir) else inputVcf
+    vcfFile = addSnpVariantRecalibrator(vcfFile, outputDir)
+    vcfFile = addIndelVariantRecalibrator(vcfFile, outputDir)
+  }
+
+  def addSnpVariantRecalibrator(inputVcf: File, dir: String): File = {
+    val snpRecal = VariantRecalibrator(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal"),
+      swapExt(dir, inputVcf, ".vcf", ".indel.tranches"), indel = false)
+    if (!snpRecal.resource.isEmpty) {
+      add(snpRecal)
+
+      val snpApply = ApplyRecalibration(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal.vcf"),
+        snpRecal.recal_file, snpRecal.tranches_file, indel = false)
+      add(snpApply)
+
+      return snpApply.out
+    } else {
+      logger.warn("Skipped snp Recalibration, resource is missing")
+      return inputVcf
+    }
+  }
+
+  def addIndelVariantRecalibrator(inputVcf: File, dir: String): File = {
+    val indelRecal = VariantRecalibrator(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal"),
+      swapExt(dir, inputVcf, ".vcf", ".indel.tranches"), indel = true)
+    if (!indelRecal.resource.isEmpty) {
+      add(indelRecal)
+
+      val indelApply = ApplyRecalibration(this, inputVcf, swapExt(dir, inputVcf, ".vcf", ".indel.recal.vcf"),
+        indelRecal.recal_file, indelRecal.tranches_file, indel = true)
+      add(indelApply)
+
+      return indelApply.out
+    } else {
+      logger.warn("Skipped indel Recalibration, resource is missing")
+      return inputVcf
+    }
+  }
+
+  def addVariantAnnotator(inputvcf: File, bamfiles: List[File], dir: String): File = {
+    val variantAnnotator = VariantAnnotator(this, inputvcf, bamfiles, swapExt(dir, inputvcf, ".vcf", ".anotated.vcf"))
+    add(variantAnnotator)
+    return variantAnnotator.out
+  }
+}
+
+object GatkVariantRecalibration extends PipelineCommand

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

+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, 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
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
+import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+import scala.collection.SortedMap
+import scala.language.reflectiveCalls
+
+class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  val scriptOutput = new GatkVariantcalling.ScriptOutput
+
+  @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM")
+  var inputBams: List[File] = Nil
+
+  @Input(doc = "Raw vcf file", shortName = "raw")
+  var rawVcfInput: File = _
+
+  @Argument(doc = "Reference", shortName = "R", required = false)
+  var reference: File = config("reference", required = true)
+
+  @Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
+  var dbsnp: File = config("dbsnp")
+
+  @Argument(doc = "OutputName", required = false)
+  var outputName: String = _
+
+  @Argument(doc = "Sample name", required = false)
+  var sampleID: String = _
+
+  var preProcesBams: Option[Boolean] = config("pre_proces_bams", default = true)
+  var variantcalling: Boolean = true
+  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)
+  var useMpileup: Boolean = config("use_mpileup", default = true)
+  var useIndelRealigner: Boolean = config("use_indel_realign", default = true)
+  var useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)