diff --git a/scala/qscript/playground/BatchMerge.q b/scala/qscript/playground/BatchMerge.q
index 7eb693a34..56867b0ed 100755
--- a/scala/qscript/playground/BatchMerge.q
+++ b/scala/qscript/playground/BatchMerge.q
@@ -1,9 +1,12 @@
 import java.io.{FileReader, BufferedReader}
+import org.broadinstitute.sting.commandline.Hidden
 import org.broadinstitute.sting.datasources.pipeline.Pipeline
-import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK
+import org.broadinstitute.sting.queue.extensions.gatk._
+import org.broadinstitute.sting.queue.library.ipf.vcf.{VCFSimpleMerge, VCFExtractSites,VCFExtractIntervals}
 import org.broadinstitute.sting.queue.pipeline.{ProjectManagement, BamProcessing, VariantCalling}
 import org.broadinstitute.sting.queue.{QException, QScript}
 import collection.JavaConversions._
+import org.broadinstitute.sting.utils.baq.BAQ
 import org.broadinstitute.sting.utils.text.XReadLines
 import org.broadinstitute.sting.utils.yaml.YamlUtils
 
@@ -15,13 +18,72 @@ class batchMergePipeline extends QScript {
   @Argument(doc="sting dir",shortName="sting") var stingDir: String = _
   @Argument(doc="reference file",shortName="ref") var ref: File = _
   @Argument(doc="batched output",shortName="batch") var batchOut: File = _
+  //@Argument(doc="read UG settings from header",shortName="ugh") var ugSettingsFromHeader : Boolean = false
+  @Hidden @Argument(doc="Min base q",shortName="mbq",required=false) var mbq : Int = 20
+  @Hidden @Argument(doc="Min map q",shortName="mmq",required=false) var mmq : Int = 20
+  @Hidden @Argument(doc="Max mismatching bases",shortName="mmb",required=false) var mmb : Int = 3
+  @Hidden @Argument(doc="baq gap open penalty, using sets baq to calc when necessary",shortName="baqp",required=false) var baq : Int = -1
 
   def script = {
 
     var vcfs : List[File] = extractFileEntries(vcfList)
     var bams : List[File] = extractFileEntries(bamList)
-    var pmLib = new ProjectManagement(stingDir)
-    addAll(pmLib.MergeBatches(vcfs,bams,batchOut,ref,20))
+
+    trait ExtractArgs extends VCFExtractSites {
+      this.keepFilters = true
+      this.keepInfo = false
+      this.keepQual = false
+    }
+
+    var getVariantAlleles : List[VCFExtractSites] = vcfs.map( u => new VCFExtractSites(u, swapExt(batchOut.getParent,u,".vcf",".alleles.vcf")) with ExtractArgs)
+    var combineVCFs : VCFSimpleMerge = new VCFSimpleMerge
+    combineVCFs.vcfs = getVariantAlleles.map(u => u.outVCF)
+    combineVCFs.fai = new File(ref.getAbsolutePath+".fai")
+    combineVCFs.outVCF = swapExt(batchOut,".vcf",".pf.alleles.vcf")
+    var extractIntervals : VCFExtractIntervals = new VCFExtractIntervals(combineVCFs.outVCF,swapExt(combineVCFs.outVCF,".vcf",".intervals.list"),true)
+    addAll(getVariantAlleles)
+    add(combineVCFs,extractIntervals)
+
+    trait CalcLikelihoodArgs extends UGCalcLikelihoods {
+      this.reference_sequence = batchMerge.ref
+      this.max_mismatches_in_40bp_window = Some(batchMerge.mmb)
+      this.min_base_quality_score = Some(batchMerge.mbq)
+      this.min_mapping_quality_score = Some(batchMerge.mmq)
+      if ( batchMerge.baq >= 0 ) {
+        this.baqGapOpenPenalty = Some(batchMerge.baq)
+        this.baq = Some(BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
+      }
+      this.intervals :+= extractIntervals.listOut
+      this.alleleVCF = combineVCFs.outVCF
+      this.output_all_callable_bases = true
+      this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar")
+      this.memoryLimit = Some(4)
+      this.scatterCount = 60
+    }
+
+    def newUGCL( bams: (List[File],Int) ) : UGCalcLikelihoods = {
+      var ugcl = new UGCalcLikelihoods with CalcLikelihoodArgs
+      ugcl.input_file ++= bams._1
+      ugcl.out = new File("MBatch%d.likelihoods.vcf".format(bams._2))
+      return ugcl
+    }
+
+    var calcs: List[UGCalcLikelihoods] = bams.grouped(20).toList.zipWithIndex.map(u => newUGCL(u))
+    addAll(calcs)
+
+    trait CallVariantsArgs extends UGCallVariants {
+      this.output_all_callable_bases = true
+      this.reference_sequence = batchMerge.ref
+      this.intervals :+= extractIntervals.listOut
+      this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar")
+      this.scatterCount = 30
+      this.memoryLimit = Some(8)
+    }
+
+    var cVars : UGCallVariants = new UGCallVariants with CallVariantsArgs
+    cVars.rodBind ++= calcs.map( a => new RodBind("variant"+a.out.getName.replace(".vcf",""),"vcf",a.out) )
+    cVars.out = batchOut
+    add(cVars)
   }
 
   def extractFileEntries(in: File): List[File] = {
diff --git a/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala b/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
index ffb4476d5..c072d219a 100755
--- a/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
+++ b/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
@@ -14,8 +14,8 @@ class VCFExtractIntervals(inVCF: File, outList: File, passOnly: Boolean ) extend
   @Argument(doc="Whether to use all sites, or only the unfiltered sites") var usePFOnly: Boolean = passOnly
 
   def commandLine = {
-    if ( usePFOnly ) "grep PASS %s | awk '{print $1\":\"$2}' > %s".format(inputVCF.getAbsolutePath,outputList.getAbsolutePath)
-    else "grep -v \\\\# %s | awk '{print $1\":\"$2}' > %s".format(inputVCF.getAbsolutePath,outputList.getAbsolutePath)
+    if ( usePFOnly ) "grep PASS %s | awk '{print $1\":\"$2}' | uniq > %s".format(inputVCF.getAbsolutePath,outputList.getAbsolutePath)
+    else "grep -v \\\\# %s | awk '{print $1\":\"$2}' | uniq > %s".format(inputVCF.getAbsolutePath,outputList.getAbsolutePath)
   }
 
 }
\ No newline at end of file
diff --git a/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala b/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
index 49d070e75..398fc37fb 100755
--- a/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
+++ b/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
@@ -24,7 +24,7 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e
 
   def vcf2int( vcfLine: String ) : Unit = {
     var spline = vcfLine.split("\t")
-    if ( ! vcfLine.startsWith("#") && (spline(6).equals("PASS") || keepFilters) ) {
+    if ( ! vcfLine.startsWith("#") && (spline(6).equals("PASS") || spline(6).equals(".") || keepFilters) ) {
       out.print("%s:%s%n".format(spline(0),spline(1)))
     }
   }
diff --git a/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala b/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
index f4d64d12d..da69761a9 100755
--- a/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
+++ b/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
@@ -16,17 +16,26 @@ class VCFExtractSites( vcf: File, output: File) extends InProcessFunction {
 
   def lineMap( line: String ) : String = {
     if ( line.startsWith("##") ) { return line }
-    val spline = line.split("\t",9)
+    var spline = line.split("\t",9)
     if ( spline(0).startsWith("#")) { return spline.slice(0,8).reduceLeft( _+"\t"+_) }
 
     if ( spline(6) == "PASS" || keepFilters ) {
-      if ( ! keepInfo ) {
-        spline(7) = "."
+      var buf = new StringBuffer(spline.slice(0,5).reduceLeft(_ + "\t" + _ ))
+      if ( keepQual ) {
+        buf.append("\t%s".format(spline(5)))
+      } else {
+        buf.append("\t.")
       }
-      if ( ! keepQual ) {
-        spline(5) = "."
+
+      buf.append("\t.")
+
+      if ( keepInfo ) {
+        buf.append("\t%s".format(spline(7)))
+      } else {
+        buf.append("\t.")
       }
-      return spline.slice(0,8).reduceLeft( _ + "\t" + _ )
+
+      return buf.toString
     }
 
     return ""
diff --git a/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala b/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
index 94b79454f..c193b63e8 100755
--- a/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
+++ b/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
@@ -66,9 +66,13 @@ class VCFSimpleMerge extends InProcessFunction {
 
     val glp : GenomeLocParser = new GenomeLocParser(ssd)
 
+    var last = ""
     while ( ! xrls.forall( u => ! u.hasNext ) ) {
       val first = xrls.filter( u => u.hasNext).reduceLeft( (a,b) => if ( genomeLoc(a,glp).isBefore(genomeLoc(b,glp))) a else b )
-      w.println(first.next)
+      if ( ! first.peek.equals(last) ) {
+        w.println(first.peek)
+      }
+      last = first.next
     }
 
     w.close
diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
index cf845a1b5..a614954a4 100755
--- a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
@@ -2,11 +2,14 @@ package org.broadinstitute.sting.queue.pipeline
 import org.broadinstitute.sting.commandline._
 import org.broadinstitute.sting.queue.util._
 import java.io.File
+import scala.collection.JavaConversions._
 import org.broadinstitute.sting.datasources.pipeline.Pipeline
 import org.broadinstitute.sting.gatk.DownsampleType
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.utils.yaml.YamlUtils
 import org.broadinstitute.sting.queue.function.CommandLineFunction
+import org.broadinstitute.sting.utils.text.XReadLines
+import scala.collection.mutable.HashMap
 
 class VariantCalling(attribs: Pipeline,gatkJar: File) {
   vc =>
@@ -370,3 +373,48 @@ class VariantCalling(attribs: Pipeline,gatkJar: File) {
     new File(file.getName.stripSuffix(oldExtension) + newExtension)
 
 }
+
+object VariantCalling {
+
+  /**
+   * @Input - a VCF file (presumably with ##UnifiedGenotyper=" ... line
+   * @Doc - Constructs a UG object based on the settings in the header of the input VCF
+   * @Returns an instance of the UG object with all information propagated
+   */
+  def unifiedGenotyperFromVCF( vcf : File ) : UnifiedGenotyper = {
+    var myUG : UnifiedGenotyper = new UnifiedGenotyper
+    var xrl : XReadLines = new XReadLines(vcf)
+    val header_limit = 1000
+    var line = ""
+    var line_no = 1
+    while ( ! line.startsWith("##UnifiedGenotyper=") && line_no < header_limit) {
+      line = xrl.next
+      line_no += 1
+    }
+    var ugLine : String = line
+    if ( ! ugLine.startsWith("##UnifiedGenotyper") ) {
+      return myUG // nothing to add
+    }
+
+    var ugTokens = ugLine.stripPrefix("##UnifiedGenotyper=\"").stripSuffix("\"").split("[^,;:] ")
+    var ugMap = new HashMap[String,String]
+    def addEntry( s : String ) : Unit = {
+      val sps = s.split("=")
+      val k = sps(0)
+      val v = sps(1)
+      val kv = (k,v)
+      ugMap += kv
+    }
+    ugTokens.foreach( addEntry(_) )
+
+    myUG.reference_sequence = new File(ugMap("reference_sequence"))
+    myUG.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.valueOf(ugMap("baq")))
+    myUG.baqGapOpenPenalty = Some(ugMap("baqGapOpenPenalty").toDouble)
+    myUG.DBSNP = new File(ugMap("DBSNP"))
+
+    // todo -- more args
+    
+    return myUG
+
+  }
+}