From 8bb92160b50b871888159e8b66f70cc301d2ba39 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 May 2011 21:19:42 +0000
Subject: [PATCH] Script to identify mendelian violations in the CEU Trio and
 follow up with supposedly incorrect SNP calls

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5744 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffs/carneiro/mendelianViolation.scala | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100755 scala/qscript/oneoffs/carneiro/mendelianViolation.scala

diff --git a/scala/qscript/oneoffs/carneiro/mendelianViolation.scala b/scala/qscript/oneoffs/carneiro/mendelianViolation.scala
new file mode 100755
index 000000000..e285bfa60
--- /dev/null
+++ b/scala/qscript/oneoffs/carneiro/mendelianViolation.scala
@@ -0,0 +1,56 @@
+import java.io.File
+import org.broadinstitute.sting.commandline.Argument
+import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, RodBind}
+import org.broadinstitute.sting.queue.QScript
+
+/*
+* Created by IntelliJ IDEA.
+* User: carneiro
+* Date: 4/12/11
+* Time: 11:24 AM
+*/
+
+class mendelianViolation extends QScript
+{
+
+  @Argument(shortName="trio", doc="input trio VCF file", required=false)
+  var trio: File = new File("/home/radon00/carneiro/prj/trio/analysis/calls/CEUTrio.WEx.recalibrated.vcf")
+
+  @Argument(shortName="daughter", doc="daughter input VCF file", required=false)
+  var daughter: File = "/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/NA12878/chart/sting/NA12878.HiSeq19.recalibrated.hapmapCut.vcf"
+
+  @Argument(shortName="family", doc="family string", required=false)
+  var family: String = "NA12891+NA12892=NA12878"
+
+  @Argument(shortName="mvq", doc="mendelian violation quality", required=false)
+  var mvq: Double = 20
+
+  @Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=false)
+  var GATKjar: File = new File("/humgen/gsa-scr1/carneiro/stable/dist/GenomeAnalysisTK.jar")
+
+  def script = {
+    val reference = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
+    val trioViolations = "trio_violations.vcf"
+    val daughterViolations = "daughter_violations.vcf"
+
+    val mv = new SelectVariants()
+    mv.rodBind :+= RodBind("variant", "VCF", trio)
+    mv.family = family
+    mv.reference_sequence = reference
+    mv.mvq = mvq
+    mv.out = trioViolations
+    mv.jarFile = GATKjar
+    mv.memoryLimit = 4
+
+    val intersection = new SelectVariants()
+    intersection.rodBind :+= RodBind("variant", "VCF", daughter)
+    intersection.rodBind :+= RodBind("conc","VCF", trioViolations)
+    intersection.reference_sequence = reference
+    intersection.conc = "conc"
+    intersection.out = daughterViolations
+    intersection.jarFile = GATKjar
+    intersection.memoryLimit = 4
+
+    add(mv, intersection)
+  }
+}