diff --git a/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala
index a32ced012..a9e278054 100755
--- a/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala
+++ b/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala
@@ -16,20 +16,56 @@ class MethodsDevelopmentCallingPipeline extends QScript {
   @Argument(shortName="skipCalling", doc="If true, skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false)
   var skipCalling: Boolean = false
 
+  @Argument(shortName="dataset", doc="selects the datasets to run. If not provided, all datasets will be used", required=false)
+  var datasets: List[String] = Nil
+
+  @Argument(shortName="skipGoldStandard", doc="runs the pipeline with the goldstandard VCF files for comparison", required=false)
+  var skipGoldStandard: Boolean = false
+
+  @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false)
+  var noBAQ: Boolean = false
+
+  @Argument(shortName="noMASK", doc="turns off MASK calculation", required=false)
+  var noMASK: Boolean = false
+
+  @Argument(shortName="eval", doc="adds the VariantEval walker to the pipeline", required=false)
+  var eval: Boolean = false
+
+
   trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3); }
 
-  class Target(val baseName: String, val reference: File, val rodName: String, val bamList: File, val goldStandard_VCF: File, val intervals: String, val titvTarget: Double, val isLowpass: Boolean) {
-    def name = qscript.outputDir + baseName
-    def clusterFile = new File(name + ".clusters")
-    def rawVCF = new File(name + ".raw.vcf")
-    def filteredVCF = new File(name + ".filtered.vcf")
-    def goldStandardName = qscript.outputDir + "goldStandard/" + baseName
-    def goldStandardClusterFile = new File(goldStandardName + ".clusters")
+  class Target(
+          val baseName: String,
+          val reference: File,
+          val dbsnpFile: String,
+          val hapmapFile: String,
+          val maskFile: String,
+          val bamList: File,
+          val goldStandard_VCF: File,
+          val intervals: String,
+          val titvTarget: Double,
+          val isLowpass: Boolean) {
+    val name = qscript.outputDir + baseName
+    val clusterFile = new File(name + ".clusters")
+    val rawVCF = new File(name + ".raw.vcf")
+    val filteredVCF = new File(name + ".filtered.vcf")
+    val titvRecalibratedVCF = new File(name + ".titv.recalibrated.vcf")
+    val tsRecalibratedVCF = new File(name + ".ts.recalibrated.vcf")
+    val goldStandardName = qscript.outputDir + "goldStandard/" + baseName
+    val goldStandardClusterFile = new File(goldStandardName + ".clusters")
   }
 
   val hg18 = new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
   val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta")
   val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
+  val dbSNP_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_hg18.rod"
+  val dbSNP_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_b36.rod"
+  val dbSNP_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132_b37.leftAligned.vcf"
+  val hapmap_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.hg18_fwd.vcf"
+  val hapmap_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b36_fwd.vcf"
+  val hapmap_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf"
+  val indelMask_b36 = "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b36.bed"
+  val indelMask_b37 = "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b37.bed"
 
   // ToDos:
   // reduce the scope of the datasets so the script is more nimble
@@ -41,8 +77,48 @@ class MethodsDevelopmentCallingPipeline extends QScript {
   // spike in NA12878 to the exomes and to the lowpass, analysis of how much of her variants are being recovered compared to single sample exome or HiSeq calls
   // produce Kiran's Venn plots based on comparison between new VCF and gold standard produced VCF
 
-  // Define the target datasets here
-  def lowPass = true
+  val lowPass: Boolean = true
+
+  val targetDataSets: Map[String, Target] = Map(
+    "HiSeq" -> new Target("NA12878.HiSeq", hg18, dbSNP_hg18, hapmap_hg18,
+              "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask",
+              new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"),
+              new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"),
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, !lowPass),
+    "FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
+              new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
+              new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"),         // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
+    "WEx" -> new Target("NA12878.WEx", hg18, dbSNP_hg18, hapmap_hg18,
+              "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask",
+              new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"),
+              new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"),
+              "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, !lowPass),
+    "TGPWExGdA" -> new Target("1000G.WEx.GdA", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
+              new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"),        // BUGBUG: reduce from 60 to 20 people
+              new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
+              "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass),
+    "LowPassN60" -> new Target("lowpass.N60", b36, dbSNP_b36, hapmap_b36, indelMask_b36,
+              new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/lowpass.chr20.cleaned.matefixed.bam"), // the bam list to call from
+              new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"),           // the gold standard VCF file to run through the VQSR
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, lowPass),          // chunked interval list to use with Queue's scatter/gather functionality
+    "LowPassAugust" -> new Target("ALL.august.v4", b37, dbSNP_b37, hapmap_b37, indelMask_b37,                               // BUGBUG: kill this, it is too large
+              new File("/humgen/1kg/processing/allPopulations_chr20_august_release.cleaned.merged.bams/ALL.cleaned.merged.list"),
+              new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"),
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
+    "LowPassEUR363Nov" -> new Target("EUR.nov2010", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
+              new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"),
+              new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"),         // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
+              "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
+    "WExTrio" -> new Target("NA12878Trio.WEx", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
+        new File("/humgen/gsa-scr1/carneiro/prj/trio/NA12878Trio.WEx.hg19.bam"),
+        new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
+        "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass)
+  )
+
+  /*
+  // OLD TARGET DATABASES -- TO BE REMOVED.
+
   val HiSeq = new Target("NA12878.HiSeq", hg18, "hg18", // BUGBUG: cut down to chr1
         new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"),
         new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"),
@@ -71,26 +147,44 @@ class MethodsDevelopmentCallingPipeline extends QScript {
         new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"), // BUGBUG: reduce from 60 to 20 people
         new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
         "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass)
+  val WExTrio = new Target("NA12878Trio.WEx", b37, "b37",
+        new File("/humgen/gsa-scr1/carneiro/prj/trio/NA12878Trio.WEx.hg19.bam"),
+        new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
+        "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass)
 
-  val targets = List(HiSeq, WEx, LowPassN60, LowPassAugust, LowPassEUR363Nov, LowPassFIN79Nov, TGPWExGdA)
+  //val targets = List(HiSeq, WEx, LowPassN60, LowPassAugust, LowPassEUR363Nov, LowPassFIN79Nov, TGPWExGdA)
   //val targets = List(HiSeq, WEx, LowPassEUR363Nov, LowPassFIN79Nov)
   //val targets = List(LowPassFIN79Nov)
 
+  */
+
   def script = {
-      def goldStandard = true
-      for (target <- targets) {
-        if( !skipCalling ) {
-          add(new UnifiedGenotyper(target))
-          add(new VariantFiltration(target))
-          add(new GenerateVariantClusters(target, !goldStandard))
-          add(new VariantRecalibratorTiTv(target, !goldStandard))
-          add(new VariantRecalibratorNRS(target, !goldStandard))
-        }
-        
+
+    // Selects the datasets in the -dataset argument and adds them to targets.
+    var targets: List[Target] = List()
+    if (!datasets.isEmpty)
+      for (ds <- datasets)
+        targets ::= targetDataSets(ds)                  // Could check if ds was mispelled, but this way an exception will be thrown, maybe it's better this way?
+    else                                                // If -dataset is not specified, all datasets are used.
+      for (targetDS <- targetDataSets.valuesIterator)   // for Scala 2.7 or older, use targetDataSets.values
+        targets ::= targetDS
+
+    val goldStandard = true
+    for (target <- targets) {
+      if( !skipCalling ) {
+        add(new UnifiedGenotyper(target))
+        add(new VariantFiltration(target))
+        add(new GenerateVariantClusters(target, !goldStandard))
+        add(new VariantRecalibratorTiTv(target, !goldStandard))
+        add(new VariantRecalibratorNRS(target, !goldStandard))
+        if (eval) add(new VariantEvaluation(target))
+      }
+      if ( !skipGoldStandard ) {
         add(new GenerateVariantClusters(target, goldStandard))
         add(new VariantRecalibratorTiTv(target, goldStandard))
         add(new VariantRecalibratorNRS(target, goldStandard))
       }
+    }
   }
 
   def bai(bam: File) = new File(bam + ".bai")
@@ -100,7 +194,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
   // 1.) Call SNPs with UG
   class UnifiedGenotyper(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
     this.reference_sequence = t.reference
-    this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
     this.intervalsString ++= List(t.intervals)
     this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
     this.dcov = Some( if ( t.isLowpass ) { 50 } else { 250 } )
@@ -108,8 +201,12 @@ class MethodsDevelopmentCallingPipeline extends QScript {
     this.stand_emit_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } )
     this.input_file :+= t.bamList
     this.out = t.rawVCF
-    this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE)
+    this.baq = Some( if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE})
     this.analysisName = t.name + "_UG"
+    if (t.dbsnpFile.endsWith(".rod"))
+      this.DBSNP = new File(t.dbsnpFile)
+    else if (t.dbsnpFile.endsWith(".vcf"))
+      this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
   }
 
   // 2.) Filter SNPs
@@ -119,22 +216,22 @@ class MethodsDevelopmentCallingPipeline extends QScript {
     this.scatterCount = 10
     this.variantVCF = t.rawVCF
     this.out = t.filteredVCF
-    this.rodBind :+= RodBind("mask", "Bed", "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask." + t.rodName + ".bed")
-    this.maskName = "InDel"
     this.filterName ++= List("HARD_TO_VALIDATE")
     this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
     this.analysisName = t.name + "_VF"
+    if (!noMASK) {
+      this.rodBind :+= RodBind("mask", "Bed", t.maskFile)
+      this.maskName = "InDel"
+    }
   }
 
   // 3.) VQSR part1 Generate Gaussian clusters based on truth sites
   class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters with UNIVERSAL_GATK_ARGS {
       val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
       this.reference_sequence = t.reference
-      this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
-      this.rodBind :+= RodBind("hapmap", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
-      if( t.rodName.equals("b37") ) {
+      this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
+      if( t.hapmapFile.contains("b37") )
         this.rodBind :+= RodBind("1kg", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf")
-      }
       this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
       this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
       this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
@@ -144,18 +241,20 @@ class MethodsDevelopmentCallingPipeline extends QScript {
       this.std = Some(3.5)
       this.mG = Some(10)
       this.ignoreFilter ++= FiltersToIgnore
+      if (t.dbsnpFile.endsWith(".rod"))
+        this.DBSNP = new File(t.dbsnpFile)
+      else if (t.dbsnpFile.endsWith(".vcf"))
+        this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
   }
 
   // 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters
   class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator with UNIVERSAL_GATK_ARGS {
       val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
       this.reference_sequence = t.reference
-      this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
-      this.rodBind :+= RodBind("hapmap", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
-      if( t.rodName.equals("b37") ) {
+      if( t.hapmapFile.contains("b37") )
         this.rodBind :+= RodBind("1kg", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf")
-      }
-      this.rodBind :+= RodBind("truth", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
+      this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
+      this.rodBind :+= RodBind("truth", "VCF", t.hapmapFile)
       this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
       this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
       this.analysisName = name + "_VR"
@@ -163,6 +262,10 @@ class MethodsDevelopmentCallingPipeline extends QScript {
       this.ignoreFilter ++= FiltersToIgnore
       this.ignoreFilter ++= List("HARD_TO_VALIDATE")
       this.target_titv = t.titvTarget
+      if (t.dbsnpFile.endsWith(".rod"))
+        this.DBSNP = new File(t.dbsnpFile)
+      else if (t.dbsnpFile.endsWith(".vcf"))
+        this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
   }
 
   // 4a.) Choose VQSR tranches based on novel ti/tv
@@ -182,4 +285,22 @@ class MethodsDevelopmentCallingPipeline extends QScript {
       this.prior1KG = Some(2.0)    
       this.tranchesFile = new File(this.name + ".ts.tranches")
   }
+
+  // 5.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf
+  class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval with UNIVERSAL_GATK_ARGS {
+      val name: String = t.name
+      this.reference_sequence = t.reference
+      this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
+      this.rodBind :+= RodBind("eval", "VCF", t.tsRecalibratedVCF)
+      this.analysisName = name + "_VR"
+      this.intervalsString ++= List(t.intervals)
+      this.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R)
+      this.reportLocation = new File(t.name + ".eval")
+      this.noStandard = true
+      this.evalModule ++= List("TiTvVariantEvaluator", "CountVariants", "GenotypeConcordance")
+      if (t.dbsnpFile.endsWith(".rod"))
+        this.DBSNP = new File(t.dbsnpFile)
+	    else if (t.dbsnpFile.endsWith(".vcf"))
+        this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
+  }
 }