Commit 5dad53d7 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Generate bamstats on the dedup

parent e1eb4765
...@@ -28,6 +28,7 @@ import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount ...@@ -28,6 +28,7 @@ import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaIndex, SambambaMerge, SambambaMarkdup } import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaIndex, SambambaMerge, SambambaMarkdup }
import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Delly, CleverCaller } import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Delly, CleverCaller }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
...@@ -94,19 +95,21 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript { ...@@ -94,19 +95,21 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
// When the sample has only 1 run, make a link in the main alignment directory // When the sample has only 1 run, make a link in the main alignment directory
val alignmentlink = Ln(this, libraryBamfiles.head, val alignmentlink = Ln(this, libraryBamfiles.head,
alignmentDir + sampleID + ".merged.bam", true) alignmentDir + sampleID + ".merged.bam", true)
add(alignmentlink, isIntermediate = true) add(alignmentlink, isIntermediate=true)
alignmentlink.out alignmentlink.out
} else if (libraryBamfiles.size > 1) { } else if (libraryBamfiles.size > 1) {
val mergeSamFiles = new SambambaMerge(this) val mergeSamFiles = new SambambaMerge(this)
mergeSamFiles.input = libraryBamfiles mergeSamFiles.input = libraryBamfiles
mergeSamFiles.output = alignmentDir + sampleID + ".merged.bam" mergeSamFiles.output = alignmentDir + sampleID + ".merged.bam"
add(mergeSamFiles, isIntermediate = true) add(mergeSamFiles, isIntermediate=true)
mergeSamFiles.output mergeSamFiles.output
} else null } else null
val bamMarkDup = SambambaMarkdup(this, bamFile) val bamMarkDup = SambambaMarkdup(this, bamFile)
add(bamMarkDup) add(bamMarkDup)
addAll(BamMetrics(this, bamMarkDup.output, alignmentDir + "metrics/").functions)
// create an IGV TDF file // create an IGV TDF file
val tdfCount = IGVToolsCount(this, bamMarkDup.output, config("genomename", default = "hg19")) val tdfCount = IGVToolsCount(this, bamMarkDup.output, config("genomename", default = "hg19"))
add(tdfCount) add(tdfCount)
......
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