diff --git a/scala/qscript/oneoffs/delangel/Phase1IndelVQSR.scala b/scala/qscript/oneoffs/delangel/Phase1IndelVQSR.scala
new file mode 100755
index 000000000..45cc45148
--- /dev/null
+++ b/scala/qscript/oneoffs/delangel/Phase1IndelVQSR.scala
@@ -0,0 +1,241 @@
+import collection.SeqLike._
+import management.CompilationMXBean
+import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.IndelStatistics
+import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection
+import org.broadinstitute.sting.queue.extensions.gatk._
+import org.broadinstitute.sting.queue.extensions.gatk.RodBind._
+import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
+import org.broadinstitute.sting.queue.QScript
+import org.apache.commons.io.FilenameUtils
+import scala.Some
+;
+
+class Phase1IndelVQSR extends QScript {
+  qscript =>
+  // todo -- update to released version when things stabilize
+  @Argument(shortName = "gatk",doc="gatkJarFile", required=false)
+  var gatkJarFile: File = new File("/humgen/gsa-scr1/delangel/Sting_dev/dist/GenomeAnalysisTK.jar")
+
+  @Argument(shortName = "R", doc="B37 reference sequence: defaults to broad standard location", required=false)
+  var referenceFile: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
+
+  @Argument(shortName = "intervals", doc="intervals to evaluate.  Only supports evaluation on chromosome 20 now, as most evaluation data is there", required=false)
+  val TARGET_INTERVAL: String = "20"
+
+  @Argument(shortName = "dataDir", doc="Path to the standard evaluation data files", required=false)
+  val DATA_DIR = "/humgen/gsa-hpprojects/GATK/data/Comparisons/StandardForEvaluation/b37/"
+  @Argument(shortName = "baseDir", doc="Path to the standard evaluation data files", required=false)
+  val baseDir = "/humgen/gsa-scr1/delangel/VQSRIndels/data/"
+
+  @Argument(shortName = "outDir", doc="Path to the output files", required=false)
+  val OUT_DIR = "/humgen/gsa-scr1/delangel/VQSRIndels"
+
+  @Argument(shortName = "truth", doc="VQSR truth file", required=false)
+  var truthFile: File = new File("/humgen/gsa-scr1/delangel/devine_data/indel_hg19_051711_leftAligned_75percent_chr20.vcf"  )
+  val populations = List("EUR","AMR","ASN","AFR")
+
+  @Argument(shortName = "evalStandard1000GCalls", doc="If provided, we'll include some standard 1000G data for evaluation", required=false)
+  val EVAL_STANDARD_1000G_CALLS: Boolean = true
+
+  @Argument(shortName = "numG", doc="If provided, we'll include some standard 1000G data for evaluation", required=false)
+  val numG: Int = 4
+
+  @Argument(shortName = "pctBad", doc="If provided, we'll include some standard 1000G data for evaluation", required=false)
+    val pctBad: Double = 0.05
+
+  @Argument(shortName = "runName", doc="Run Name", required=false)
+  val runName:String = "mills100"
+  val COMPS_DIR = DATA_DIR + "comps/"
+  val EVALS_DIR = DATA_DIR + "evals/"
+
+  @Argument(shortName = "createAllPos", doc="If provided, create all POPS file", required=false)
+  val CREATE_ALL_POPS_FILE: Boolean = false
+
+  @Argument(shortName = "pops", doc="Populations to do", required=false)
+  val moreIndelsToEval: List[String] = List("EUR","ASN","AFR","AMR")
+
+
+  val VARIANT_TYPES: List[String] = List("indels", "snps")
+
+  val VARIANT_TYPE_VT: Map[String, List[org.broad.tribble.util.variantcontext.VariantContext.Type]] = Map(
+    "indels" -> List(org.broad.tribble.util.variantcontext.VariantContext.Type.INDEL, org.broad.tribble.util.variantcontext.VariantContext.Type.MIXED, org.broad.tribble.util.variantcontext.VariantContext.Type.NO_VARIATION),
+    "snps" -> List(org.broad.tribble.util.variantcontext.VariantContext.Type.SNP, org.broad.tribble.util.variantcontext.VariantContext.Type.NO_VARIATION)
+  )
+
+  val SITES_DIR: String = "sitesFiles"
+
+  // path to b37 DBSNP
+  val MY_DBSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.leftAligned.vcf")
+
+  var COMPS: List[Comp] = Nil
+  def addComp(comp: Comp) { COMPS = comp :: COMPS }
+
+  var EVALS: List[Eval] = Nil
+  def addEval(eval: Eval) { EVALS = eval :: EVALS }
+  def addEvalFromCMD(file: File, t: String) { addEval(new Eval(file.getName, t, file.getName)) }
+
+  trait CommandLineGATKArgs extends CommandLineGATK {
+    this.jarFile = qscript.gatkJarFile
+    this.reference_sequence = qscript.referenceFile
+    this.memoryLimit = Some(2)
+    // this.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP )
+    this.jobQueue = "week"
+    this.intervalsString = List(TARGET_INTERVAL);
+
+  }
+  class Comp(val name: String, val evalType: String, val filename: String) {
+    val file: File = new File(filename)
+  }
+
+  class Eval(val name: String, val evalType: String, val filename: String ) {
+    val file: File = new File(filename)
+  }
+
+  def initializeStandardDataFiles() = {
+    //
+    // Standard evaluation files for indels
+    //
+    //addComp(new Comp("CG.38samples", "indels", COMPS_DIR+"CG.Indels.leftAligned.b37.vcf"))
+    addComp(new Comp("g1k.pilot1.validation", "indels", COMPS_DIR+"pilot1_indel_validation_2009.b37.vcf"))
+    //addComp(new Comp("NA12878.hand_curated", "indels", "NA12878.validated.curated.polymorphic.indels.vcf"))
+    addComp(new Comp("NA12878.Mullikin", "indels", COMPS_DIR+"NA12878.DIPline.NQScm.expanded.chr20.b37.minReads_2_or_gt2bp.vcf"))
+    addComp(new Comp("Mills.25pct", "indels", "/humgen/gsa-scr1/delangel/devine_data/indel_hg19_051711_leftAligned_25percent_chr20.vcf"))
+    addComp(new Comp("Phase1Validation", "indels", "/humgen/gsa-scr1/delangel/VQSRIndels/1KG_Validation_Phase1_SNPs_05032011.HG19.finalized.vcf"))
+
+
+    //
+    // INDEL call sets
+    //
+
+    if ( EVAL_STANDARD_1000G_CALLS ) {
+//      addEval(new Eval("dindel", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf"))
+      addEval(new Eval("si", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20101123.chr20.si.v2.combined.sites.leftAligned.vcf"))
+      addEval(new Eval("bi", "indels", "/humgen/1kg/processing/official_release/phase1/ALL.wgs.broad.20101123.indels.sites.vcf"))
+      addEval(new Eval("bc", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/ALL.chr20.bc.20101123.indels.sites.leftAligned.vcf"))
+      addEval(new Eval("ox", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.chr20.Oxford.20110407.indels.genotypes.sites.vcf"))
+      addEval(new Eval("2of5", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.2of5.chr20.vcf"))
+      }
+
+    //
+    // Standard evaluation files for SNPs
+    //
+    /*   addComp(new Comp("NA12878.homvar.GATK", "snps", "NA12878.HiSeq19.cut.vcf", true))
+    addComp(new Comp("CG.38samples", "snps", "CG.38samples.b37.vcf"))
+    addComp(new Comp("NA12878.homvar.CG", "snps", "NA12878.CG.b37.snps.vcf", true))
+    addComp(new Comp("HapMap3.3", "snps", "hapmap3.3.sites_r27_nr.b37_fwd.vcf"))
+    addComp(new Comp("OMNI.2.5M", "snps", "omni2.5.1212samples.b37.sites.chr20.monoAreAC0.vcf"))
+    addComp(new Comp("g1k.pilot1.validation", "snps", "1000G.snp.validation.b37.vcf"))
+    */
+    //
+    // SNP call sets
+    //
+  }
+
+  def script = {
+
+    initializeStandardDataFiles();
+
+    // add additional files for evaluation, if necessary
+    //moreSNPsToEval.foreach(addEvalFromCMD(_, "snps"))
+    //moreIndelsToEval.foreach(addEvalFromCMD(_, "indels"))
+
+
+    var ts:Double = 0.0
+    var tranches =  List("99.9","99.0","98.0","97.0","95.0","92.0","90.0")
+
+    var numG:Int = qscript.numG
+    var pctBad:Double = qscript.pctBad
+    val runName:String = qscript.runName +  "_mG%d_pb%1.2f_QD_FS_HS_RP_IC".format(numG,pctBad)
+
+    for( pop <- qscript.populations ) {
+      val rawCalls = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/%s/%s.phase1.chr20.raw.indels.vcf".format(pop,pop))
+      //val filteredCalls = new File(baseName + ".v5."+runStr+".filtered.vcf")
+      // val runname =
+      //val clusterFile = new File(baseName + ".omni.clusters")
+      //val recalibratedCalls = new File(baseName + ".recal.vcf")
+      var tranchesFile = new File(qscript.baseDir +"%s_%s.tranches".format(pop,runName))
+      var recalFile = new File(qscript.baseDir +"%s_%s.recal".format(pop,runName))
+      var rscriptFile = new File(qscript.baseDir +"%s_%s.plots.R".format(pop,runName))
+
+
+
+      var vr = new VariantRecalibrator with CommandLineGATKArgs
+      vr.rodBind :+= RodBind("input", "VCF",rawCalls )
+      vr.rodBind :+= RodBind("truth", "VCF",qscript.truthFile,"known=true,training=true,truth=true,prior=20.0" )
+      vr.mode = VariantRecalibratorArgumentCollection.Mode.INDEL
+      vr.tranchesFile = tranchesFile
+      vr.recalFile = recalFile
+      vr.rscriptFile = rscriptFile
+      vr.an = List("QD","FS","HaplotypeScore","ReadPosRankSum","InbreedingCoeff")
+      vr.maxGaussians = Some(numG)
+      vr.tranche = tranches
+      vr.nt = Some(8)
+      vr.percentBad = Some(pctBad)
+      add(vr)
+
+
+      for (tas: String <- tranches) {
+        ts = tas.toDouble
+        val outFile = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/%s/%s.phase1.chr20.recal_%s_ts_%4.1f.indels.sites.vcf".format(pop,pop,runName,ts))
+
+        var ar = new ApplyRecalibration with CommandLineGATKArgs
+        ar.rodBind :+= RodBind("input", "VCF",rawCalls )
+        ar.mode = VariantRecalibratorArgumentCollection.Mode.INDEL
+        ar.tranchesFile = tranchesFile
+        ar.recalFile = recalFile
+        ar.ts_filter_level = Some(ts)
+        ar.sites_only = true
+        ar.o = outFile
+        add(ar)
+      }
+    }
+
+
+    val VE = new MyEval()
+    VE.VT = VARIANT_TYPE_VT("indels")
+    VE.o = new File(OUT_DIR+"/"+ runName + ".eval")
+    //VE.nt = Some(8)
+
+    for (tas: String <- tranches) {
+      ts = tas.toDouble
+      var cm = new CombineVariants with CommandLineGATKArgs
+
+      cm.o = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/ALL.phase1.chr20.recal_%s_ts_%4.1f.indels.sites.vcf".format(runName,ts))
+      for( pop <- qscript.populations ) {
+        val outFile = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/%s/%s.phase1.chr20.recal_%s_ts_%4.1f.indels.sites.vcf".format(pop,pop,runName,ts))
+        cm.rodBind :+= RodBind(pop, "VCF", outFile)
+      }
+      add(cm)
+
+      VE.rodBind :+= RodBind("eval_ts%4.1f".format(ts), "VCF", cm.o)
+
+    }
+    // add evals
+    for ( calls <- EVALS )
+      VE.rodBind :+= RodBind("eval_" + calls.name, "VCF", calls.file)
+
+    // add comps
+//    VE.rodBind :+= RodBind("dbsnp", "VCF", MY_DBSNP)
+    for ( comp <- COMPS )
+      VE.rodBind :+= RodBind("comp_" + comp.name, "VCF", comp.file)
+
+    add(VE)
+
+   }
+
+
+  /**
+   * Base class for VariantEval used here
+   */
+  class MyEval() extends VariantEval with CommandLineGATKArgs {
+    this.noST = true
+    this.evalModule :+= "ValidationReport"
+    //this.evalModule :+= "IndelMetricsByAC"
+    this.evalModule :+= "IndelStatistics"
+    this.evalModule :+= "CountVariants"
+    //this.evalModule :+= "IndelClasses"
+  }
+
+
+
+}