Merge remote-tracking branch 'origin/develop' into develop

biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py

@@ -30,19 +30,21 @@ import csv
 import datetime
 
 
-def main(tsvfile, vcffile):
+def main(tsvfile, vcffile, samplename):
     '''
     :param tsvfile: filename of input file.tsv
     :type tsvfile: string
     :param vcffile: filename of output file.vcf
     :type vcffile: string
+    :param samplename: Name of the sample
+    :type samplename: string
     '''
     with open(tsvfile) as reader:
         # Parse file
         dictreader = _parse_tsvfile(reader)
 
         # Write out file
-        _format_vcffile(dictreader, vcffile)
+        _format_vcffile(dictreader, vcffile, samplename)
 
 def _parse_tsvfile(readable):
     '''
@@ -92,11 +94,11 @@ _tsv_fields = ('Chr1', 'Pos1', 'Orientation1',
 
 
 
-_vcf_fields = ('CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'default')
+_vcf_fields = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT']
 
 TS_NOW = datetime.datetime.now()
 
-VCF_HEADER = """##fileformat=VCFv4.1
+VCF_HEADER = """##fileformat=VCFv4.2
 ##fileDate={filedate}
 ##source=breakdancer-max
 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
@@ -106,6 +108,7 @@ VCF_HEADER = """##fileformat=VCFv4.1
 ##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
 ##INFO=<ID=SVEND,Number=1,Type=Integer,Description="End position of the variant described in this record">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=SVMETHOD,Number=0,Type=String,Description="Program called with">
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
@@ -138,7 +141,7 @@ VCF_HEADER = """##fileformat=VCFv4.1
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">""".format( filedate=TS_NOW.strftime( "%Y%m%d" ) )
 
-def _format_vcffile(dictreader, vcffile):
+def _format_vcffile(dictreader, vcffile, samplename):
     '''
     Create a pseudo .vcf file based on values read from DictReader instance.
     :param dictreader: DictReader instance to read data from
@@ -148,22 +151,22 @@ def _format_vcffile(dictreader, vcffile):
     '''
     FORMAT = "GT:DP"
     with open(vcffile, mode='w') as writer:
-        writer.write('{header}\n#{columns}\n'.format(header=VCF_HEADER, columns='\t'.join(_vcf_fields)))
+        writer.write('{header}\n#{columns}\n'.format(header=VCF_HEADER, columns='\t'.join(_vcf_fields + [samplename])))
         output_vcf = []
         for line in dictreader:
             CHROM = line['Chr1']
             # TODO Figure out whether we have zero or one based positioning
             POS = int(line['Pos1'])
-            ALT = '.'
+            ALT = '<{}>'.format(line['Type'])
             SVEND = int(line['Pos2'])
 
-            INFO = 'PROGRAM=breakdancer;SVTYPE={}'.format(line['Type'])
+            INFO = 'SVMETHOD=breakdancer;SVTYPE={}'.format(line['Type'])
 
             if line['Type'] not in ['CTX']:
                 INFO += ';SVLEN={}'.format(int(line['Size']))
                 INFO += ";SVEND={}".format(SVEND)
                 INFO += ";END={}".format(SVEND)
-            
+
             # write alternate ALT field for Intrachromosomal translocations
             if line['Type'] in ['CTX']:
                 ALT = "N[{}:{}[".format(line['Chr2'], line['Pos2'])
@@ -172,7 +175,7 @@ def _format_vcffile(dictreader, vcffile):
 
             SAMPLEINFO = "{}:{}".format( '1/.', line['num_Reads'] )
             # Create record
-            output_vcf.append([CHROM, POS, '.', '.', ALT, '.', 'PASS', INFO, FORMAT, SAMPLEINFO])
+            output_vcf.append([CHROM, POS, '.', 'N', ALT, '.', 'PASS', INFO, FORMAT, SAMPLEINFO])
 
         # Sort all results
         output_vcf.sort()
@@ -184,9 +187,11 @@ def _format_vcffile(dictreader, vcffile):
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser.add_argument('-i', '--breakdancertsv', dest='breakdancertsv', type=str,
-            help='Breakdancer TSV outputfile')
+                        help='Breakdancer TSV outputfile')
     parser.add_argument('-o', '--outputvcf', dest='outputvcf', type=str,
-            help='Output vcf to')
+                        help='Output vcf to')
+    parser.add_argument('-s', '--sample', dest='sample', type=str,
+                        help='sample name')
 
     args = parser.parse_args()
-    main(args.breakdancertsv, args.outputvcf)
+    main(args.breakdancertsv, args.outputvcf, args.sample)

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala

@@ -64,7 +64,7 @@ class Pysvtools(val root: Configurable) extends BiopetCommandLineFunction {
 
   /** return commandline to execute */
   def cmdLine = required(executable) +
-    repeat("-c", input) +
+    repeat("-c", exclusionRegions) +
     optional("-f", flanking) +
     "-i " + repeat(input) +
     "-o " + required(tsvoutput) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala

@@ -19,7 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import org.broadinstitute.gatk.utils.commandline._
 
 class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("breakdancer2vcf.py")
@@ -30,18 +30,23 @@ class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
   @Output(doc = "Output VCF to PATH")
   var output: File = _
 
+  @Argument(doc = "Samplename")
+  var sample: String = _
+
   def cmdLine = {
     getPythonCommand +
       "-i " + required(input) +
-      "-o " + required(output)
+      "-o " + required(output) +
+      "-s " + required(sample)
   }
 }
 
 object BreakdancerVCF {
-  def apply(root: Configurable, input: File, output: File): BreakdancerVCF = {
+  def apply(root: Configurable, input: File, output: File, sample: String): BreakdancerVCF = {
     val bd = new BreakdancerVCF(root)
     bd.input = input
     bd.output = output
+    bd.sample = sample
     bd
   }
 }
\ No newline at end of file

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala

@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.extensions.clever
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ Version, Reference, BiopetCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
   executable = config("exe", default = "clever")
@@ -39,17 +39,17 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
   @Input(doc = "Reference")
   var reference: File = _
 
-  protected def workDir: File = new File(cwd, "work")
-  var cwd: File = _
+  protected def cleverOutputDir: File = new File(cleverWorkDir, "work")
+  var cleverWorkDir: File = _
 
   @Output(doc = "Clever VCF output")
   lazy val outputvcf: File = {
-    new File(cwd, "predictions.vcf")
+    new File(cleverOutputDir, "predictions.vcf")
   }
 
   @Output(doc = "Clever raw output")
   lazy val outputraw: File = {
-    new File(workDir, "predictions.raw.txt")
+    new File(cleverOutputDir, "predictions.raw.txt")
   }
 
   //  var T: Option[Int] = config("T", default = defaultThreads)
@@ -61,7 +61,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
 
   override def beforeGraph() {
     super.beforeGraph()
-    if (workDir == null) throw new Exception("Clever :: Workdirectory is not defined")
+    if (cleverOutputDir == null) throw new Exception("Clever :: Workdirectory is not defined")
     if (reference == null) reference = referenceFasta()
   }
 
@@ -75,14 +75,14 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
     conditional(r, "-r") +
     required(input) +
     required(reference) +
-    required(workDir)
+    required(cleverOutputDir)
 }
 
 object CleverCaller {
   def apply(root: Configurable, input: File, svDir: File): CleverCaller = {
     val clever = new CleverCaller(root)
     clever.input = input
-    clever.cwd = svDir
+    clever.cleverWorkDir = svDir
     clever
   }
 }
\ No newline at end of file

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala

+package nl.lumc.sasc.biopet.extensions.clever
+
+/**
+ * Created by wyleung on 4-4-16.
+ */
+
+import java.io.{ File, PrintWriter }
+
+import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
+import scala.io.Source
+
+class CleverFixVCF(val root: Configurable) extends BiopetJavaCommandLineFunction {
+  javaMainClass = getClass.getName
+  @Input(doc = "Input Clever VCF")
+  var input: File = _
+
+  @Output(doc = "Output fixed VCF")
+  var output: File = _
+
+  @Argument(doc = "Samplename")
+  var sampleName: String = _
+
+  override def cmdLine = super.cmdLine +
+    required("-i", input) +
+    required("-o", output) +
+    required("-s", sampleName)
+}
+
+object CleverFixVCF extends ToolCommand {
+  case class Args(inputVCF: File = null, sampleLabel: String = "",
+                  outputVCF: File = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('i', "inputvcf") required () valueName "<vcffile/path>" action { (x, c) =>
+      c.copy(inputVCF = x)
+    } text "Please specify the input Clever VCF file"
+    opt[String]('s', "samplelabel") valueName "<sample label>" action { (x, c) =>
+      c.copy(sampleLabel = x)
+    } text "Sample label is missing"
+    opt[File]('o', "outputvcf") valueName "<output>" action { (x, c) =>
+      c.copy(outputVCF = x)
+    } text "Output path is missing"
+  }
+
+  def replaceHeaderLine(inHeaderLine: String, toCheckFor: String, replacement: String, extraHeader: String): String = {
+    (inHeaderLine == toCheckFor) match {
+      case true => {
+        extraHeader + "\n" + replacement + "\n"
+      }
+      case _ => {
+        // We have to deal with matching records
+        // these don't start with #
+
+        inHeaderLine.startsWith("#") match {
+          case true =>
+            inHeaderLine + "\n"
+          case _ => {
+            // this should be a record
+            // Ensure the REF field is at least an N
+            val cols = inHeaderLine.split("\t")
+            cols(3) = "N"
+            cols.mkString("\t") + "\n"
+          }
+        }
+      }
+    }
+  }
+
+  val extraHeader = """##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
+##INFO=<ID=SVEND,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
+##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
+##INFO=<ID=METRANS,Number=4,Type=String,Description="Mobile element transduction info of the form CHR,START,END,POLARITY">
+##INFO=<ID=DGVID,Number=1,Type=String,Description="ID of this element in Database of Genomic Variation">
+##INFO=<ID=DBVARID,Number=1,Type=String,Description="ID of this element in DBVAR">
+##INFO=<ID=DBRIPID,Number=1,Type=String,Description="ID of this element in DBRIP">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=BPWINDOW,Number=2,Type=Integer,Description="Window of breakpoints">
+##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the inserted material between breakends">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
+##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">
+##INFO=<ID=CN,Number=1,Type=Integer,Description="Copy number of segment containing breakend">
+##INFO=<ID=CNADJ,Number=.,Type=Integer,Description="Copy number of adjacency">
+##INFO=<ID=CICN,Number=2,Type=Integer,Description="Confidence interval around copy number for the segment">
+##INFO=<ID=CICNADJ,Number=.,Type=Integer,Description="Confidence interval around copy number for the adjacency">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood for imprecise events">
+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">
+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">"""
+
+  val vcfColHeader = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tdefault"
+
+  val vcfColReplacementHeader = s"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t"
+  /**
+   * @param args the command line arguments
+   */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+
+    val input: File = commandArgs.inputVCF
+    val output: File = commandArgs.outputVCF
+
+    val inputVCF = Source.fromFile(input)
+    val writer = new PrintWriter(output)
+    inputVCF.getLines().foreach(x =>
+      writer.write(replaceHeaderLine(x, vcfColHeader, vcfColReplacementHeader + commandArgs.sampleLabel, extraHeader))
+    )
+    writer.close()
+    inputVCF.close()
+  }
+}
+

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala

@@ -31,14 +31,14 @@ class PindelConfig(val root: Configurable) extends BiopetJavaCommandLineFunction
   var output: File = _
 
   @Argument(doc = "Insertsize")
-  var insertSize: Int = _
+  var insertSize: Int = 0
 
   var sampleName: String = _
 
   override def cmdLine = super.cmdLine +
     required("-i", input) +
     required("-n", sampleName) +
-    required("-s", insertSize) +
+    { if (insertSize == 0) "" else s" -s $insertSize " } +
     required("-o", output)
 }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala

@@ -81,7 +81,6 @@ class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with R
     required("--reference", reference) +
     required("--reference_name", referenceSpecies) +
     required("--reference_date", rDate) +
-    required("--fake_biopet_input_holder", pindelOutputInputHolder) +
     optional("--pindel_output", pindelOutput) +
     optional("--pindel_output_root", pindelOutputRoot) +
     required("--vcf", outputVCF) +

biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/clever/test.clever.vcf

+##fileformat=VCFv4.2
+##fileDate=20150730
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	default
+chrM	352	L170961	N	<DEL>	.	PASS	BPWINDOW=353,16175;CILEN=15817,15829;IMPRECISE;SVLEN=-15823;SVTYPE=DEL	GT:DP	1/.:76

biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala

+package nl.lumc.sasc.biopet.extensions.clever
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+import scala.io.Source
+
+/**
+ * Created by wyleung on 13-5-16.
+ */
+class CleverFixVCFTest extends TestNGSuite with Matchers {
+
+  /** Returns the absolute path to test resource directory as a File object */
+  private[clever] val resourceDir: File = new File(Paths.get(getClass.getResource(".").toURI).toString)
+
+  /** Given a resource file name, returns the the absolute path to it as a File object */
+  private[clever] def resourceFile(p: String): File = new File(resourceDir, p)
+
+  val rawCleverVCF = resourceFile("test.clever.vcf")
+  val expectedCleverVCF = resourceFile("expectedresult.clever.vcf")
+
+  @Test
+  def replacementSucces = {
+    CleverFixVCF.replaceHeaderLine(
+      CleverFixVCF.vcfColHeader,
+      CleverFixVCF.vcfColHeader,
+      CleverFixVCF.vcfColReplacementHeader + "testsample",
+      CleverFixVCF.extraHeader
+    ) should equal(CleverFixVCF.extraHeader + "\n" + CleverFixVCF.vcfColReplacementHeader + "testsample" + "\n")
+  }
+
+  @Test
+  def replacementOther = {
+    val vcfRecord = "chrM\t312\tL743020\t.\t<DEL>\t.\tPASS\tBPWINDOW=313,16189;CILEN=15866,15888;IMPRECISE;SVLEN=-15877;SVTYPE=DEL\tGT:DP\t1/.:103"
+    val vcfRecordExpected = "chrM\t312\tL743020\tN\t<DEL>\t.\tPASS\tBPWINDOW=313,16189;CILEN=15866,15888;IMPRECISE;SVLEN=-15877;SVTYPE=DEL\tGT:DP\t1/.:103"
+    CleverFixVCF.replaceHeaderLine(
+      vcfRecord,
+      CleverFixVCF.vcfColHeader,
+      CleverFixVCF.vcfColReplacementHeader + "testsample",
+      CleverFixVCF.extraHeader
+    ) should equal(vcfRecordExpected + "\n")
+  }
+
+  @Test
+  def mainTest = {
+    val output = File.createTempFile("clever", ".test.vcf")
+    output.deleteOnExit()
+
+    val result = CleverFixVCF.main(Array(
+      "-i", rawCleverVCF.getAbsolutePath,
+      "-o", output.getAbsolutePath,
+      "-s", "testsample"
+    ))
+
+    val exp = Source.fromFile(expectedCleverVCF).getLines()
+    val obs = Source.fromFile(output).getLines()
+
+    (exp zip obs).foreach(_ match {
+      case (a, b) => {
+        a shouldEqual (b)
+      }
+      case _ =>
+    })
+  }
+
+  @Test
+  def javaCommand = {
+    val output = File.createTempFile("clever", ".test.vcf")
+    output.deleteOnExit()
+    val cfvcf = new CleverFixVCF(null)
+    cfvcf.input = rawCleverVCF
+    cfvcf.output = output
+    cfvcf.sampleName = "testsample"
+
+    cfvcf.cmdLine should include("'-s' 'testsample'")
+    cfvcf.cmdLine should include(s"'-i' '${rawCleverVCF}'")
+    cfvcf.cmdLine should include(s"'-o' '${output}'")
+  }
+}

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala

@@ -15,7 +15,8 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerVCF, BreakdancerCaller, BreakdancerConfig }
+import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
+import nl.lumc.sasc.biopet.extensions.picard.SortVcf
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caler Breakdancer */
@@ -31,10 +32,16 @@ class Breakdancer(val root: Configurable) extends SvCaller {
 
       val bdcfg = BreakdancerConfig(this, bamFile, new File(breakdancerSampleDir, sample + ".breakdancer.cfg"))
       val breakdancer = BreakdancerCaller(this, bdcfg.output, new File(breakdancerSampleDir, sample + ".breakdancer.tsv"))
-      val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"))
-      add(bdcfg, breakdancer, bdvcf)
+      val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"),
+        sample = sample + sampleNameSuffix)
 
-      addVCF(sample, bdvcf.output)
+      val compressedVCF = new SortVcf(this)
+      compressedVCF.input = bdvcf.output
+      compressedVCF.output = new File(breakdancerSampleDir, s"${sample}.breakdancer.vcf.gz")
+
+      add(bdcfg, breakdancer, bdvcf, compressedVCF)
+
+      addVCF(sample, compressedVCF.output)
     }
   }
 }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala

@@ -15,7 +15,8 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
+import nl.lumc.sasc.biopet.extensions.clever.{ CleverCaller, CleverFixVCF }
+import nl.lumc.sasc.biopet.extensions.picard.SortVcf
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caler Clever */
@@ -29,7 +30,19 @@ class Clever(val root: Configurable) extends SvCaller {
       val clever = CleverCaller(this, bamFile, cleverDir)
       add(clever)
 
-      addVCF(sample, clever.outputvcf)
+      val cleverVCF = new CleverFixVCF(this)
+      cleverVCF.input = clever.outputvcf
+      cleverVCF.output = new File(cleverDir, s".${sample}.clever.vcf")
+      cleverVCF.sampleName = sample + sampleNameSuffix
+      cleverVCF.isIntermediate = true
+      add(cleverVCF)
+
+      val compressedVCF = new SortVcf(this)
+      compressedVCF.input = cleverVCF.output
+      compressedVCF.output = new File(cleverDir, s"${sample}.clever.vcf.gz")
+      add(compressedVCF)
+
+      addVCF(sample, compressedVCF.output)
     }
   }
 }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
 import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
 import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
+import nl.lumc.sasc.biopet.extensions.picard.SortVcf
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caller delly */
@@ -41,7 +42,13 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.analysistype = "DEL"
         delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
         add(delly)
-        catVariants.variant :+= delly.outputvcf
+
+        val compressedVCF = new SortVcf(this)
+        compressedVCF.input = delly.outputvcf
+        compressedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
+        add(compressedVCF)
+
+        catVariants.variant :+= compressedVCF.output
       }
       if (dup) {
         val delly = new DellyCaller(this)
@@ -49,7 +56,13 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.analysistype = "DUP"
         delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
         add(delly)
-        catVariants.variant :+= delly.outputvcf
+
+        val compressedVCF = new SortVcf(this)
+        compressedVCF.input = delly.outputvcf
+        compressedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
+        add(compressedVCF)
+
+        catVariants.variant :+= compressedVCF.output
       }
       if (inv) {
         val delly = new DellyCaller(this)
@@ -57,18 +70,30 @@ class Delly(val root: Configurable) extends SvCaller {
         delly.analysistype = "INV"
         delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
         add(delly)
-        catVariants.variant :+= delly.outputvcf
+