Merge branch 'develop' into fix-BIOPET-655

basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

@@ -98,7 +98,7 @@ class BastyTest extends TestNGSuite with Matchers {
       val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0)
       val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)
 
-      pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample2) 1 else 0))
+      pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + numberSamples)
 
       // Gatk preprocess
       pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))

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

@@ -56,6 +56,8 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
   @Argument(fullName = "maxGGAARExtension", shortName = "maxGGAARExtension", doc = "the maximum extent into the full active region extension that we're willing to go in genotyping our events for GGA mode", required = false, exclusiveOf = "", validation = "")
   var maxGGAARExtension: Option[Int] = config("maxGGAARExtension")
 
+  var useNewAFCalculator: Boolean = config("useNewAFCalculator", default = false)
+
   /** Include at least this many bases around an event for calling indels */
   @Argument(fullName = "paddingAroundIndels", shortName = "paddingAroundIndels", doc = "Include at least this many bases around an event for calling indels", required = false, exclusiveOf = "", validation = "")
   var paddingAroundIndels: Option[Int] = config("paddingAroundIndels")
@@ -441,6 +443,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
     optional("-paddingAroundSNPs", paddingAroundSNPs, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
+    conditional(useNewAFCalculator, "--useNewAFCalculator") +
     repeat("-XA", excludeAnnotation, spaceSeparated = true, escape = true, format = "%s") +
     repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
     conditional(debug, "-debug", escape = true, format = "%s") +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala

@@ -25,6 +25,6 @@ abstract class Sambamba extends BiopetCommandLineFunction with Version {
 
   executable = config("exe", default = "sambamba", namespace = "sambamba", freeVar = false)
   def versionCommand = executable
-  def versionRegex = """sambamba v(.*)""".r
+  def versionRegex = """sambamba v?(.*)""".r
   override def versionExitcode = List(0, 1)
 }
\ No newline at end of file

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala

@@ -21,7 +21,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for sambemba markdup  */
 class SambambaMarkdup(val parent: Configurable) extends Sambamba {
-  override def defaultThreads = 4
 
   @Input(doc = "Bam File")
   var input: File = _
@@ -32,17 +31,29 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
   var removeDuplicates: Boolean = config("remove_duplicates", default = false)
 
   // @doc: compression_level 6 is average, 0 = no compression, 9 = best
-  val compressionLevel: Option[Int] = config("compression_level", default = 6)
-  val hashTableSize: Option[Int] = config("hash-table-size", default = 262144)
-  val overflowListSize: Option[Int] = config("overflow-list-size", default = 200000)
-  val ioBufferSize: Option[Int] = config("io-buffer-size", default = 128)
+  val compressionLevel: Option[Int] = config("compression_level")
+  val hashTableSize: Option[Int] = config("hash-table-size")
+  val overflowListSize: Option[Int] = config("overflow-list-size")
+  val ioBufferSize: Option[Int] = config("io-buffer-size")
+  val showProgress: Boolean = config("show-progress", default = true)
+
+  override def defaultThreads = 4
+  override def defaultCoreMemory = 4.0
+
+  @Output
+  private var indexOutput: File = _
+
+  override def beforeGraph(): Unit = {
+    indexOutput = new File(output + ".bai")
+  }
 
   /** Returns command to execute */
-  def cmdLine = required(executable) +
+  def cmdLine: String = required(executable) +
     required("markdup") +
     conditional(removeDuplicates, "--remove-duplicates") +
     optional("-t", nCoresRequest) +
     optional("-l", compressionLevel) +
+    conditional(showProgress, "--show-progress") +
     optional("--hash-table-size=", hashTableSize, spaceSeparated = false) +
     optional("--overflow-list-size=", overflowListSize, spaceSeparated = false) +
     optional("--io-buffer-size=", ioBufferSize, spaceSeparated = false) +
@@ -51,10 +62,11 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
 }
 
 object SambambaMarkdup {
-  def apply(root: Configurable, input: File, output: File): SambambaMarkdup = {
+  def apply(root: Configurable, input: File, output: File, isIntermediate: Boolean = false): SambambaMarkdup = {
     val markdup = new SambambaMarkdup(root)
     markdup.input = input
     markdup.output = output
+    markdup.isIntermediate = isIntermediate
     markdup
   }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala

@@ -21,7 +21,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for sambemba merge  */
 class SambambaMerge(val parent: Configurable) extends Sambamba {
-  override def defaultThreads = 4
 
   @Input(doc = "Bam File[s]")
   var input: List[File] = Nil
@@ -30,13 +29,29 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
   var output: File = _
 
   // @doc: compression_level 6 is average, 0 = no compression, 9 = best
-  val compressionLevel: Option[Int] = config("compression_level", default = 6)
+  val compressionLevel: Option[Int] = config("compression_level")
+  val header: Boolean = config("header", default = false)
+  val showProgress: Boolean = config("show-progress", default = true)
+  val filter: Option[String] = config("filter")
+
+  override def defaultThreads = 4
+  override def defaultCoreMemory = 4.0
+
+  @Output
+  private var indexOutput: File = _
+
+  override def beforeGraph(): Unit = {
+    indexOutput = new File(output + ".bai")
+  }
 
   /** Returns command to execute */
-  def cmdLine = required(executable) +
+  def cmdLine: String = required(executable) +
     required("merge") +
     optional("-t", nCoresRequest) +
     optional("-l", compressionLevel) +
+    optional("-F", filter) +
+    conditional(header, "--header") +
+    conditional(showProgress, "--show-progress") +
     required(output) +
-    repeat("", input)
+    repeat(input)
 }

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStatsForSv.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
+ * 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.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
+class VcfStatsForSv(val parent: Configurable) extends ToolCommandFunction with Summarizable {
+  def toolObject = nl.lumc.sasc.biopet.tools.vcfstats.VcfStatsForSv
+
+  mainFunction = false
+
+  @Input(required = true)
+  var inputFile: File = _
+
+  @Argument(required = true)
+  var histogramBinBoundaries: Array[Int] = _
+
+  @Output(required = true)
+  var outputFile: File = _
+
+  override def defaultCoreMemory = 1.0
+
+  override def cmdLine = super.cmdLine +
+    required("-i", inputFile) +
+    required("-o", outputFile) +
+    repeat("--histBinBoundaries", histogramBinBoundaries)
+
+  def summaryStats: Map[String, Any] = ConfigUtils.fileToConfigMap(outputFile)
+
+  def summaryFiles: Map[String, File] = Map.empty
+
+}

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsForSv.scala

+package nl.lumc.sasc.biopet.tools.vcfstats
+
+import java.io.File
+
+import htsjdk.variant.vcf.VCFFileReader
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, ToolCommand }
+
+import scala.collection.JavaConversions._
+
+object VcfStatsForSv extends ToolCommand {
+  /** Commandline arguments */
+  case class Args(inputFile: File = null, outputFile: File = null, histBinBoundaries: Array[Int] = Array()) extends AbstractArgs
+
+  /** Parsing commandline arguments */
+  class OptParser extends AbstractOptParser {
+    opt[File]('i', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(inputFile = x)
+    } validate {
+      x => if (x.exists) success else failure("Input VCF required")
+    } text "Input VCF file (required)"
+
+    opt[File]('o', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(outputFile = x)
+    } text "Output file (required)"
+
+    opt[Int]("histBinBoundaries") required () unbounded () action { (x, c) =>
+      c.copy(histBinBoundaries = c.histBinBoundaries :+ x)
+    } text "When counting the records, sv-s are divided to different size classes, this parameter should give the boundaries between these classes."
+  }
+
+  protected var cmdArgs: Args = _
+
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    logger.info(s"Parsing file: ${cmdArgs.inputFile}")
+
+    val stats: Map[String, Any] = getVariantCounts(cmdArgs.inputFile, cmdArgs.histBinBoundaries)
+
+    ConfigUtils.mapToYamlFile(stats, cmdArgs.outputFile)
+
+  }
+
+  /** Parses a vcf-file and counts sv-s by type and size. Sv-s are divided to different size classes, the parameter histogramBinBoundaries gives the boundaries between these classes. */
+  def getVariantCounts(vcfFile: File, histogramBinBoundaries: Array[Int]): Map[String, Any] = {
+    val delCounts, insCounts, dupCounts, invCounts = Array.fill(histogramBinBoundaries.size + 1) { 0 }
+    var traCount = 0
+
+    val reader = new VCFFileReader(vcfFile, false)
+    for (record <- reader) {
+      record.getAttributeAsString("SVTYPE", "") match {
+        case "TRA" | "CTX" | "ITX" => traCount += 1
+        case svType => {
+          val size = record.getEnd - record.getStart
+          var i = 0
+          while (i < histogramBinBoundaries.size && size > histogramBinBoundaries(i)) i += 1
+          svType match {
+            case "DEL" => delCounts(i) += 1
+            case "INS" => insCounts(i) += 1
+            case "DUP" => dupCounts(i) += 1
+            case "INV" => invCounts(i) += 1
+            case _     => logger.warn(s"Vcf file contains a record of unknown type: file-$vcfFile, type-$svType")
+          }
+        }
+      }
+    }
+    reader.close()
+
+    Map("DEL" -> delCounts, "INS" -> insCounts, "DUP" -> dupCounts, "INV" -> invCounts, "TRA" -> traCount)
+  }
+
+}

biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R

@@ -13,6 +13,11 @@ parser$add_argument('--llabel', dest='llabel', type='character')
 parser$add_argument('--title', dest='title', type='character')
 parser$add_argument('--hideLegend', dest='hideLegend', type='character', default="false")
 parser$add_argument('--removeZero', dest='removeZero', type='character', default="false")
+parser$add_argument('--xLog10', dest='xLog10', type='character', default="false")
+parser$add_argument('--yLog10', dest='yLog10', type='character', default="false")
+
+parser$add_argument('--xLog10Breaks', dest='xLog10Breaks', nargs='+', type='integer')
+parser$add_argument('--xLog10Labels', dest='xLog10Labels', nargs='+', type='character')
 
 arguments <- parser$parse_args()
 
@@ -31,14 +36,29 @@ DF1 <- melt(DF, id.var="Rank")
 if (arguments$removeZero == "true") DF1 <- DF1[DF1$value > 0, ]
 if (arguments$removeZero == "true") print("Removed 0 values")
 
-ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
+plot = ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
   xlab(xlab) +
   ylab(arguments$ylabel) +
-  guides(fill=guide_legend(title=arguments$llabel)) +
+  guides(color=guide_legend(title=arguments$llabel)) +
   theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
   ggtitle(arguments$title) +
   theme_bw() +
   theme(legend.position = legendPosition) +
   geom_line()
 
+
+if (arguments$xLog10 == "true") {
+  if (!is.null(arguments$xLog10Labels)) {
+    scale_x <- scale_x_log10(breaks = arguments$xLog10Breaks, labels=arguments$xLog10Labels)
+  } else {
+    scale_x <- scale_x_log10()
+  }
+  plot <- plot + scale_x
+}
+if (arguments$yLog10 == "true") {
+  plot <- plot + scale_y_log10()
+}
+
+plot
+
 dev.off()

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala

@@ -17,7 +17,6 @@ package nl.lumc.sasc.biopet.utils.intervals
 import java.io.{ File, PrintWriter }
 
 import htsjdk.samtools.SAMSequenceDictionary
-import htsjdk.samtools.reference.FastaSequenceFile
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable
@@ -112,6 +111,15 @@ case class BedRecordList(val chrRecords: Map[String, List[BedRecord]], val heade
     allRecords.foreach(writer.println)
     writer.close()
   }
+
+  /** This return the fraction of the regions comparing to a length */
+  def fractionOf(length: Long): Double = length.toDouble / length
+
+  /** This return the fraction of the regions comparing to a reference */
+  def fractionOfReference(dict: SAMSequenceDictionary): Double = fractionOf(dict.getReferenceLength)
+
+  /** This return the fraction of the regions comparing to a reference */
+  def fractionOfReference(file: File): Double = fractionOfReference(FastaUtils.getCachedDict(file))
 }
 
 object BedRecordList {
@@ -131,6 +139,32 @@ object BedRecordList {
 
   def fromList(records: TraversableOnce[BedRecord]): BedRecordList = fromListWithHeader(records, Nil)
 
+  /**
+   * This creates a [[BedRecordList]] based on multiple files. This method combines overlapping regions
+   *
+   * @param bedFiles Input bed files
+   * @return
+   */
+  def fromFilesCombine(bedFiles: File*) = {
+    fromFiles(bedFiles, combine = true)
+  }
+
+  /**
+   * This creates a [[BedRecordList]] based on multiple files
+   *
+   * @param bedFiles Input bed files
+   * @param combine When true overlaping regions are merged
+   * @return
+   */
+  def fromFiles(bedFiles: Seq[File], combine: Boolean = false) = {
+    val list = bedFiles.foldLeft(empty)((a, b) => fromList(fromFile(b).allRecords ++ a.allRecords))
+    if (combine) list.combineOverlap
+    else list
+  }
+
+  /** This created a empty [[BedRecordList]] */
+  def empty = fromList(Nil)
+
   def fromFile(bedFile: File) = {
     val reader = Source.fromFile(bedFile)
     val all = reader.getLines().toList

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala

@@ -39,6 +39,13 @@ class LinePlot(val parent: Configurable) extends Rscript {
   var hideLegend: Boolean = config("hide_legend", default = false)
   var removeZero: Boolean = config("removeZero", default = false)
 
+  // whether to use log scale for x and y axis
+  var xLog10: Boolean = false
+  var yLog10: Boolean = false
+
+  var xLog10AxisTicks: Seq[String] = Seq.empty
+  var xLog10AxisLabels: Seq[String] = Seq.empty
+
   override def cmd = super.cmd ++
     Seq("--input", input.getAbsolutePath) ++
     Seq("--output", output.getAbsolutePath) ++
@@ -49,7 +56,11 @@ class LinePlot(val parent: Configurable) extends Rscript {
     llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
     title.map(Seq("--title", _)).getOrElse(Seq()) ++
     (if (hideLegend) Seq("--hideLegend", "true") else Seq()) ++
-    (if (removeZero) Seq("--removeZero", "true") else Seq())
+    (if (removeZero) Seq("--removeZero", "true") else Seq()) ++
+    (if (xLog10) Seq("--xLog10", "true") else Seq()) ++
+    (if (yLog10) Seq("--yLog10", "true") else Seq()) ++
+    (if (xLog10AxisTicks.nonEmpty) xLog10AxisTicks.+:("--xLog10Breaks") else Seq()) ++
+    (if (xLog10AxisLabels.nonEmpty) xLog10AxisLabels.+:("--xLog10Labels") else Seq())
 }
 
 object LinePlot {

docs/pipelines/shiva.md

@@ -118,6 +118,11 @@ At this moment the following variant callers can be used
 | shiva | correct_readgroups | Boolean | false | Attempt to correct read groups | Only used when input is a bam file |
 | shiva | amplicon_bed | Path |  | Path to target bed file | all |
 | shiva | regions_of_interest | Array of paths |  | Array of paths to region of interest (e.g. gene panels) bed files | all |
+| shivavariantcalling | gender_aware_calling | Boolean | false | Enables gander aware variantcalling | haplotypecaller_gvcf |
+| shivavariantcalling | hap̦loid_regions | Bed file |  | Haploid regions for all genders | haplotypecaller_gvcf |
+| shivavariantcalling | hap̦loid_regions_male | Bed file |  | Haploid regions for males | haplotypecaller_gvcf |
+| shivavariantcalling | hap̦loid_regions_female | Bed file |  | Haploid regions for females | haplotypecaller_gvcf |
+| shiva | amplicon_bed | Path |  | Path to target bed file | all |
 | vcffilter | min_sample_depth | Integer | 8 | Filter variants with at least x coverage | raw |
 | vcffilter | min_alternate_depth | Integer | 2 | Filter variants with at least x depth on the alternate allele | raw |
 | vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) | raw |
@@ -130,6 +135,14 @@ For all the options, please see the corresponding documentation for the mapping
 
 ## Advanced usage
 
+### Gender aware variantcalling
+
+In Shiva and ShivaVariantcalling while using haplotypecaller_gvcf it is possible to do gender aware variantcalling. In this mode it required to supply bed files to define haploid regions (see config values). 
+- For males, `hap̦loid_regions` and `hap̦loid_regions_male` is used.
+- For females, `hap̦loid_regions` and `hap̦loid_regions_female` is used.
+
+The pipeline will use a union of those files. At least 1 file is required while using this mode.
+
 ### Reporting modes
 
 Shiva furthermore supports three modes. The default and recommended option is `multisample_variantcalling`.

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala

@@ -19,7 +19,7 @@ import java.io.File
 import htsjdk.samtools.SamReaderFactory
 import htsjdk.samtools.reference.FastaSequenceFile
 import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, MultiSampleQScript }
+import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
@@ -28,8 +28,8 @@ import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
-
 import MultisampleMapping.MergeStrategy
+import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMarkdup, SambambaMerge }
 
 import scala.collection.JavaConversions._
 
@@ -125,7 +125,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
       } else None
 
       def bamFile: Option[File] = mapping match {
-        case Some(m)                 => Some(m.finalBamFile)
+        case Some(m)                 => Some(m.mergedBamFile)
         case _ if inputBam.isDefined => Some(new File(libDir, s"$sampleId-$libId.bam"))
         case _                       => None
       }
@@ -247,9 +247,9 @@ trait MultisampleMappingTrait extends MultiSampleQScript
 
       mergeStrategy match {
         case MergeStrategy.None =>
-        case (MergeStrategy.MergeSam | MergeStrategy.MarkDuplicates) if libraries.flatMap(_._2.bamFile).size == 1 =>
+        case (MergeStrategy.MergeSam) if libraries.flatMap(_._2.bamFile).size == 1 =>
           add(Ln.linkBamFile(qscript, libraries.flatMap(_._2.bamFile).head, bamFile.get): _*)
-        case (MergeStrategy.PreProcessMergeSam | MergeStrategy.PreProcessMarkDuplicates) if libraries.flatMap(_._2.preProcessBam).size == 1 =>
+        case (MergeStrategy.PreProcessMergeSam) if libraries.flatMap(_._2.preProcessBam).size == 1 =>
           add(Ln.linkBamFile(qscript, libraries.flatMap(_._2.preProcessBam).head, bamFile.get): _*)
         case MergeStrategy.MergeSam =>
           add(MergeSamFiles(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = !keepMergedFiles))
@@ -259,6 +259,20 @@ trait MultisampleMappingTrait extends MultiSampleQScript
           add(MarkDuplicates(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = !keepMergedFiles))
         case MergeStrategy.PreProcessMarkDuplicates =>
           add(MarkDuplicates(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get, isIntermediate = !keepMergedFiles))
+        case MergeStrategy.PreProcessSambambaMarkdup =>
+          val mergedBam = if (libraries.flatMap(_._2.bamFile).size == 1) {
+            add(Ln.linkBamFile(qscript, libraries.flatMap(_._2.preProcessBam).head, new File(sampleDir, "merged.bam")): _*)
+            libraries.flatMap(_._2.preProcessBam).head
+          } else {
+            val merge = new SambambaMerge(qscript)
+            merge.input = libraries.flatMap(_._2.preProcessBam).toList
+            merge.output = new File(sampleDir, "merged.bam")
+            merge.isIntermediate = true
+            add(merge)
+            merge.output
+          }
+          add(SambambaMarkdup(qscript, mergedBam, bamFile.get, isIntermediate = !keepMergedFiles))
+          add(Ln(qscript, bamFile.get + ".bai", bamFile.get.getAbsolutePath.stripSuffix(".bam") + ".bai"))
         case _ => throw new IllegalStateException("This should not be possible, unimplemented MergeStrategy?")
       }
 
@@ -301,7 +315,7 @@ class MultisampleMapping(val parent: Configurable) extends QScript with Multisam
 object MultisampleMapping extends PipelineCommand {
 
   object MergeStrategy extends Enumeration {
-    val None, MergeSam, MarkDuplicates, PreProcessMergeSam, PreProcessMarkDuplicates = Value
+    val None, MergeSam, MarkDuplicates, PreProcessMergeSam, PreProcessMarkDuplicates, PreProcessSambambaMarkdup = Value
   }
 
   /** When file is not absolute an error is raise att the end of the script of a pipeline */

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

@@ -20,6 +20,7 @@ import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
 import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles }
+import nl.lumc.sasc.biopet.extensions.sambamba.SambambaMarkdup
 import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
@@ -91,16 +92,22 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
       pipeline.script()
 
       val numberFastqLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0) + (if (sample3 && bamToFastq) 1 else 0) + (if (sample4 && bamToFastq) 1 else 0)
-      val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)
+      val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0) + (if (sample4) 1 else 0)
 
       val pipesJobs = pipeline.functions.filter(_.isInstanceOf[BiopetCommandLineFunction])
         .flatMap(_.asInstanceOf[BiopetCommandLineFunction].pipesJobs)
 
+      if (merge == MultisampleMapping.MergeStrategy.PreProcessMarkDuplicates) {
+        ""
+      }
+
       import MultisampleMapping.MergeStrategy
       pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberFastqLibs +
-        (if (sample2 && (merge == MergeStrategy.MarkDuplicates || merge == MergeStrategy.PreProcessMarkDuplicates)) 1 else 0))
+        (if (merge == MergeStrategy.MarkDuplicates || merge == MergeStrategy.PreProcessMarkDuplicates) numberSamples else 0))
       pipeline.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (
         (if (sample2 && (merge == MergeStrategy.MergeSam || merge == MergeStrategy.PreProcessMergeSam)) 1 else 0))
+      pipeline.functions.count(_.isInstanceOf[SambambaMarkdup]) shouldBe
+        (if (merge == MergeStrategy.PreProcessSambambaMarkdup) numberSamples else 0)
       pipeline.samples.foreach {
         case (sampleName, sample) =>
           if (merge == MergeStrategy.None) sample.bamFile shouldBe None
@@ -211,6 +218,7 @@ object MultisampleMappingTestTrait {
     "sickle" -> Map("exe" -> "test"),
     "cutadapt" -> Map("exe" -> "test"),
     "bwa" -> Map("exe" -> "test"),
+    "sambamba" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),
     "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
     "wigtobigwig" -> Map("exe" -> "test"),
@@ -232,7 +240,7 @@ object MultisampleMappingTestTrait {
     )))
 
   val sample2 = Map(
-    "samples" -> Map("sample3" -> Map("libraries" -> Map(
+    "samples" -> Map("sample2" -> Map("libraries" -> Map(
       "lib1" -> Map(
         "R1" -> inputTouch("2_1_R1.fq"),
         "R2" -> inputTouch("2_1_R2.fq")

shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariantsSv.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
+#import(java.io.File)
+<%@ var summary: SummaryDb %>
+<%@ var allSamples: Seq[Sample]%>
+<%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var runId: Int %>
+<%@ var sampleId: Option[Int] = None %>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
+<%@ var showIntro: Boolean = true %>
+
+#{
+    val sampleNames: Seq[String] = sampleId match {