diff --git a/analysis/depristo/genotypeAccuracy/commands.R b/analysis/depristo/genotypeAccuracy/commands.R
index 73cd2c372..4c49c273d 100644
--- a/analysis/depristo/genotypeAccuracy/commands.R
+++ b/analysis/depristo/genotypeAccuracy/commands.R
@@ -15,7 +15,7 @@ if ( HAVE_RAW_DATA ) {
    + geom_abline(slope=1, linetype=2))
    #   + geom_smooth(se=T, size=1.5, aes(weight=Sum)))
 } else {
-  eByComp = read.table("~/Dropbox/Analysis/genotypeAccuracy/NA12878.hm3.vcf.cgl.table.eByComp.tsv", header=T)
+  eByComp = read.table("~/Dropbox/GSA members/Analysis/genotypeAccuracy/NA12878.hm3.vcf.cgl.table.eByComp.tsv", header=T)
 }
 
 #print(subset(countsByTech, pGGivenD > 18 & pGGivenD < 22 & pGGivenDType == "QofABGivenD"))
diff --git a/scala/qscript/oneoffs/depristo/IndelCallerEvaluation.scala b/scala/qscript/oneoffs/depristo/IndelCallerEvaluation.scala
new file mode 100755
index 000000000..30c577806
--- /dev/null
+++ b/scala/qscript/oneoffs/depristo/IndelCallerEvaluation.scala
@@ -0,0 +1,113 @@
+package oneoffs.depristo
+
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
+
+class IndelCallerEvaluation extends QScript {
+  val BUNDLE = "/humgen/gsa-hpprojects/GATK/bundle/current"
+
+  @Argument(doc="gatkJarFile", required=false)
+  var gatkJarFile: File = new File("dist/GenomeAnalysisTK.jar")
+
+  @Argument(shortName = "R", doc="ref", required=false)
+  var referenceFile: File = new File(BUNDLE + "/b37/human_g1k_v37.fasta")
+
+  @Argument(shortName = "bam", doc="BAM", required=true)
+  val bams: List[File] = null;
+
+  @Argument(shortName = "intervals", doc="intervals", required=false)
+  val myIntervals: String = null;
+
+  @Argument(shortName = "dcov", doc="dcov", required=false)
+  val DCOV: Int = 250;
+
+  val dbSNP: File = new File(BUNDLE + "/b37/dbsnp_132.b37.vcf")
+
+  trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
+    this.logging_level = "INFO";
+    this.jarFile = gatkJarFile;
+    this.reference_sequence = referenceFile;
+    this.memoryLimit = 4
+
+    if ( intervals != null )
+      this.intervalsString = List(myIntervals);
+  }
+
+  trait CoFoJa extends JavaCommandLineFunction {
+    override def javaOpts = super.javaOpts //  + " -javaagent:lib/cofoja.jar"
+  }
+
+  def processOne(bam: File, gsaProduction: Boolean): File = {
+    val rawVCF = new Call(bam, gsaProduction)
+    add(rawVCF)
+
+    val filterIndels = new FilterIndels(rawVCF.out)
+    add(filterIndels)
+
+    // create a variant eval for us
+    add(new Eval(filterIndels.out))
+    return filterIndels.out
+  }
+
+  def script = {
+    for ( gsaProduction <- List(true, false)) {
+      val vcfs = bams.map(processOne(_, gsaProduction))
+
+      val combineCalls = new CombineVariants with UNIVERSAL_GATK_ARGS
+      for ( vcf <- vcfs )
+        combineCalls.rodBind :+= RodBind(vcf.getName, "VCF", vcf)
+
+      combineCalls.filteredrecordsmergetype = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
+      combineCalls.out = "combined" + productionString(gsaProduction) + ".vcf"
+      add(combineCalls)
+
+      add(new ToTable(combineCalls.out))
+    }
+  }
+
+  class FilterIndels(@Input vcf: File) extends VariantFiltration with UNIVERSAL_GATK_ARGS {
+    this.variantVCF = vcf
+    this.filterName = List("Indel_QUAL", "Indel_SB", "Indel_QD")
+    this.filterExpression = List("\"QUAL<30.0\"", "\"SB>-1.0\"", "\"QD<2.0\"")
+    this.out = swapExt(vcf,".vcf",".filtered.vcf")
+  }
+
+  class ToTable(@Input vcf: File) extends VariantsToTable with UNIVERSAL_GATK_ARGS {
+    this.rodBind :+= RodBind("variant", "VCF", vcf)
+    this.fields = List("FILTER", "set")
+    this.out = swapExt(vcf,".vcf",".table")
+    this.raw = true
+  }
+
+  class Eval(@Input vcf: File) extends VariantEval with UNIVERSAL_GATK_ARGS {
+    this.rodBind :+= RodBind("eval", "VCF", vcf)
+    if ( dbSNP.exists() )
+      this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    this.doNotUseAllStandardStratifications = true
+    this.doNotUseAllStandardModules = true
+    this.evalModule = List("CountVariants", "IndelStatistics", "CompOverlap")
+    this.stratificationModule = List("EvalRod", "CompRod", "Novelty", "Filter", "JexlExpression")
+    this.out = swapExt(vcf,".vcf",".eval")
+  }
+
+  def productionString(gsaProduction: Boolean): String = {
+    return if ( gsaProduction ) ".prod" else ".expt"
+  }
+
+  class Call(@Input(doc="foo") bam: File, gsaProduction: Boolean) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
+    @Output(doc="foo") var outVCF: File = swapExt(bam,".bam", productionString(gsaProduction) + ".indels.vcf")
+    this.input_file = List(bam)
+    this.stand_call_conf = 50.0
+    this.stand_emit_conf = 50.0
+    this.dcov = DCOV;
+    this.o = outVCF
+
+    this.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
+    this.GSA_PRODUCTION_ONLY = gsaProduction
+
+    if ( dbSNP.exists() )
+      this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+  }
+}
+