From 6d3b878dde74fc35a42a2bf59499b60d3c961d00 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Feb 2011 21:49:05 +0000
Subject: [PATCH] data processing pipeline script already does: . Local Indel
 Realignment . Mark Duplicates

will do:
. Base Quality Score Recalibration (soon)

it's working with a single BAM for testing, but will work with a list of bam files.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5250 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffs/carneiro/dataProcessing.scala     | 106 ++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100755 scala/qscript/oneoffs/carneiro/dataProcessing.scala

diff --git a/scala/qscript/oneoffs/carneiro/dataProcessing.scala b/scala/qscript/oneoffs/carneiro/dataProcessing.scala
new file mode 100755
index 000000000..05173738e
--- /dev/null
+++ b/scala/qscript/oneoffs/carneiro/dataProcessing.scala
@@ -0,0 +1,106 @@
+
+import org.broadinstitute.sting.queue.extensions.gatk._
+import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
+import org.broadinstitute.sting.queue.QScript
+
+
+class dataProcessing extends QScript {
+  qscript =>
+
+  @Input(doc="path to GATK jar", shortName="gatk", required=true)
+  var gatkJar: File = _
+
+  @Input(doc="path to MarkDuplicates jar", shortName="dedup", required=true)
+  var dedupJar: File = _
+
+  @Input(doc="input BAM file", shortName="input", required=true)
+  var inputBam: File = _
+
+  @Input(doc="output path", shortName="outputDir", required=false)
+  var outputDir: String = ""
+
+  @Input(doc="path to tmp space for storing intermediate bam files", shortName="outputTmpDir", required=false)
+  var outputTmpDir: File = _
+
+  @Input(doc="the -L interval string to be used by GATK", shortName="L", required=false)
+  var intervalString: String = ""
+
+  @Input(doc="provide a .intervals file with the list of target intervals", shortName="intervals", required=false)
+  var intervals: File = _
+
+
+  def script = {
+
+    val baseName: String        = swapExt(qscript.inputBam, ".bam", "").toString()
+    def cleanedBam: String      = baseName + ".cleaned.bam"
+    def dedupedBam: String      = baseName + ".cleaned.dedup.bam"
+    def metricsFile: String     = swapExt(qscript.inputBam, "bam", "metrics").toString()
+    def targetIntervals: String = baseName + ".indel.intervals"
+
+    val reference: File       = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
+    val dbSNP: File           = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
+    val dindelPilotCalls: String = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg.pilot_release.merged.indels.sites.hg19.vcf"
+    val dindelAFRCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/AFR.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
+    val dindelASNCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/ASN.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
+    val dindelEURCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/EUR.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
+
+    trait CommandLineGATKArgs extends CommandLineGATK {
+      this.jarFile = qscript.gatkJar
+      this.reference_sequence = reference
+      this.memoryLimit = Some(2)
+      this.jobTempDir = qscript.outputTmpDir
+    }
+
+
+    val target = new RealignerTargetCreator with CommandLineGATKArgs
+    target.memoryLimit = Some(4)
+    target.input_file :+= qscript.inputBam
+    target.out = new File(targetIntervals)
+    target.mismatchFraction = Some(0.0)
+    target.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    target.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
+    target.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
+    target.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
+    target.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
+    target.jobName = baseName + ".target"
+    if (!qscript.intervalString.isEmpty()) target.intervalsString ++= List(qscript.intervalString)
+    if (qscript.intervals != Nil) target.intervals ++= List(qscript.intervals)
+
+    // 2.) Clean without SW
+
+    val clean = new IndelRealigner with CommandLineGATKArgs
+    clean.memoryLimit = Some(4)
+    clean.input_file :+= qscript.inputBam
+    clean.targetIntervals = new File(targetIntervals)
+    clean.out = new File(cleanedBam)
+    clean.doNotUseSW = true
+    clean.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE)
+    clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    clean.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
+    clean.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
+    clean.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
+    clean.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
+    clean.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true
+    clean.jobName = baseName + ".clean"
+    if (!qscript.intervalString.isEmpty()) clean.intervalsString ++= List(qscript.intervalString)
+    if (qscript.intervals != Nil) clean.intervals ++= List(qscript.intervals)
+
+    // 3.) Mark Duplicates
+    val dedup = new PicardBamJarFunction{
+      @Input(doc="cleaned bam") var clean: File = new File(cleanedBam)
+      @Output(doc="deduped bam") var dedup: File = new File(dedupedBam)
+      override def inputBams = List(clean)
+      override def outputBam = dedup
+      override def commandLine = super.commandLine + " M=" + metricsFile
+      sortOrder = null
+    }
+    dedup.memoryLimit = Some(8)
+    dedup.jarFile = qscript.dedupJar
+    dedup.jobName = baseName + ".dedup"
+
+  //  val cov = new CountCovariates with CommandLineGATKArgs
+
+
+    add(target, clean, dedup)
+  }
+}
\ No newline at end of file