Merging SV calls - changed post-calling step in several SV-callers

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

@@ -8,20 +8,19 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline._
 
 /**
-  * Created by wyleung on 8-1-16.
-  */
+ * Created by wyleung on 8-1-16.
+ */
 class Pysvtools(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Input file", required = true)
   var input: List[File] = Nil
 
-  @Argument(doc="Set flanking amount")
+  @Argument(doc = "Set flanking amount")
   var flanking: Option[Int] = config("flanking")
 
   var exclusionRegions: List[File] = config("exclusion_regions")
   var translocationsOnly: Boolean = config("translocations_only")
 
-
   @Output(doc = "Unzipped file", required = true)
   var output: File = _
 
@@ -43,16 +42,15 @@ class Pysvtools(val root: Configurable) extends BiopetCommandLineFunction {
 
     // redefine the tsv, bed and regions output
     val outputNamePrefix = output.getAbsolutePath.stripSuffix(".vcf")
-    tsvoutput = new File(outputNamePrefix+".tsv")
-    bedoutput = new File(outputNamePrefix+".bed")
-    regionsoutput = new File(outputNamePrefix+".regions.bed")
+    tsvoutput = new File(outputNamePrefix + ".tsv")
+    bedoutput = new File(outputNamePrefix + ".bed")
+    regionsoutput = new File(outputNamePrefix + ".regions.bed")
   }
 
-
   /** return commandline to execute */
   def cmdLine = required(executable) +
     repeat("-c", input) +
-    optional( "-f", flanking ) +
+    optional("-f", flanking) +
     "-i " + repeat(input) +
     "-o " + required(tsvoutput) +
     "-b " + required(bedoutput) +

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -17,9 +17,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Delly, Breakdancer, Clever, SvCaller }
-import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
+import nl.lumc.sasc.biopet.extensions.Pysvtools
+import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Breakdancer, Clever, Delly, SvCaller }
 import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import org.broadinstitute.gatk.queue.QScript
 
 /**
@@ -62,6 +63,19 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
       add(caller)
     }
 
+    // merge VCF by sample
+    for ((sample, bamFile) <- inputBams) {
+      var sampleVcfs: List[File] = List()
+      callers.foreach { caller =>
+        sampleVcfs :+= caller.outputFiles(sample)
+      }
+      val mergeSVcalls = new Pysvtools(this)
+      mergeSVcalls.input = sampleVcfs
+      mergeSVcalls.output = new File(outputDir, sample + ".merged.vcf")
+      add(mergeSVcalls)
+      outputFiles += (sample -> mergeSVcalls.output)
+    }
+
     addSummaryJobs()
   }
 

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

@@ -18,6 +18,8 @@ class Breakdancer(val root: Configurable) extends SvCaller {
       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)
+
+      outputFiles += (sample -> bdvcf.output)
     }
   }
 }

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

@@ -13,6 +13,8 @@ class Clever(val root: Configurable) extends SvCaller {
       val cleverDir = new File(outputDir, sample)
       val clever = CleverCaller(this, bamFile, cleverDir)
       add(clever)
+
+      outputFiles += (sample -> clever.outputvcf)
     }
   }
 }

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

@@ -20,7 +20,6 @@ class Delly(val root: Configurable) extends SvCaller {
       val catVariants = new CatVariants(this)
       catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf.gz")
 
-      /// start delly and then copy the vcf into the root directory "<sample>.delly/"
       if (del) {
         val delly = new DellyCaller(this)
         delly.input = bamFile
@@ -55,6 +54,8 @@ class Delly(val root: Configurable) extends SvCaller {
       }
 
       add(catVariants)
+
+      outputFiles += (sample -> catVariants.outputFile)
     }
   }
 }