From 55e5971b3bb594528af31525f6142e6f2496f293 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Mar 2011 17:09:53 +0000
Subject: [PATCH] this is a oneoff script to clean the papuans and test
 TargetCreator and IndelRealigner with scatter gathering.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5457 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../qscript/oneoffs/carneiro/justClean.scala  | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100755 scala/qscript/oneoffs/carneiro/justClean.scala

diff --git a/scala/qscript/oneoffs/carneiro/justClean.scala b/scala/qscript/oneoffs/carneiro/justClean.scala
new file mode 100755
index 000000000..d453f619b
--- /dev/null
+++ b/scala/qscript/oneoffs/carneiro/justClean.scala
@@ -0,0 +1,69 @@
+import org.broadinstitute.sting.queue.extensions.gatk.{RealignerTargetCreator, RodBind, IndelRealigner}
+import org.broadinstitute.sting.queue.QScript
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: carneiro
+ * Date: 3/17/11
+ * Time: 11:29 AM
+ * To change this template use File | Settings | File Templates.
+ */
+
+
+class justClean extends QScript {
+
+  @Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=true)
+  var GATKjar: File = _
+
+  @Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
+  var input: File = _
+
+  @Input(doc="Reference fasta file", shortName="R", required=false)
+  var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
+
+
+  @Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
+  var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
+
+  @Input(doc="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false)
+  var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
+
+
+  val queueLogDir: String = ".qlog/"
+
+
+  def script = {
+
+    val outBam = swapExt(input, ".bam", ".Qclean.bam")
+    val tIntervals = swapExt(input, ".bam", ".Qall_indels.intervals")
+
+    val target = new RealignerTargetCreator()
+    target.input_file :+= input
+    target.out = tIntervals
+    target.reference_sequence = reference
+    target.mismatchFraction = Some(0.0)
+    target.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    target.rodBind :+= RodBind("indels", "VCF", indels)
+    target.memoryLimit = Some(6)
+    target.jobName = queueLogDir + tIntervals + ".atarget"
+    target.jarFile = GATKjar
+    target.scatterCount = 84
+    
+    val clean = new IndelRealigner()
+    clean.input_file :+= input
+    clean.targetIntervals = tIntervals
+    clean.out = outBam
+    clean.reference_sequence = reference
+    clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    clean.rodBind :+= RodBind("indels", "VCF", indels)
+    clean.doNotUseSW = true
+    clean.compress = Some(0)
+    clean.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION)  // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly!
+    clean.jobName = queueLogDir + outBam + ".clean"
+    clean.jarFile = GATKjar
+    clean.memoryLimit = Some(6)
+    clean.scatterCount = 84
+
+    add(target, clean);
+  }
+}