diff --git a/public/scala/qscript/core/RecalibrateBaseQualities.scala b/public/scala/qscript/core/RecalibrateBaseQualities.scala
new file mode 100755
index 000000000..ba13d267a
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+++ b/public/scala/qscript/core/RecalibrateBaseQualities.scala
@@ -0,0 +1,91 @@
+package core
+
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+import net.sf.samtools.SAMFileReader
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: carneiro
+ * Date: 4/20/11
+ * Time: 16:29 PM
+ */
+
+
+class RecalibrateBaseQualities 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="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=false)
+  var R: String = new File("/humgen/gsa-scr1/carneiro/stable/R")
+
+  @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")
+
+  val queueLogDir: String = ".qlog/"
+  var nContigs: Int = 0
+
+  def getNumberOfContigs(bamFile: File): Int = {
+    val samReader = new SAMFileReader(new File(bamFile))
+    return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
+  }
+
+  def script = {
+
+    nContigs = getNumberOfContigs(input)
+
+    val recalFile1: File = new File("recal1.csv")
+    val recalFile2: File = new File("recal2.csv")
+    val recalBam: File        = swapExt(input, ".bam", "recal.bam")
+    val path1: String    = "before"
+    val path2: String    = "after"
+    
+    add(cov(input, recalFile1),
+        recal(input, recalFile1, recalBam),
+        cov(recalBam, recalFile2),
+        analyzeCovariates(recalFile1, path1),
+        analyzeCovariates(recalFile2, path2))
+  }
+
+  trait CommandLineGATKArgs extends CommandLineGATK {
+    this.jarFile = GATKjar
+    this.reference_sequence = reference
+    this.memoryLimit = 4
+    this.isIntermediate = true
+  }
+
+  case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
+    this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
+    this.input_file :+= inBam
+    this.recal_file = outRecalFile
+    this.analysisName = queueLogDir + outRecalFile + ".covariates"
+    this.jobName = queueLogDir + outRecalFile + ".covariates"
+    this.scatterCount = nContigs
+  }
+
+  case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
+    this.input_file :+= inBam
+    this.recal_file = inRecalFile
+    this.out = outBam
+    this.isIntermediate = false
+    this.analysisName = queueLogDir + outBam + ".recalibration"
+    this.jobName = queueLogDir + outBam + ".recalibration"
+    this.scatterCount = nContigs
+  }
+
+  case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {
+    this.resources = R
+    this.recal_file = inRecalFile
+    this.output_dir = outPath.toString
+    this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
+    this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
+  }
+}
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