diff --git a/scala/qscript/chartl/batchMergePipeline.q b/scala/qscript/chartl/batchMergePipeline.q
new file mode 100755
index 000000000..b00dfe7c0
--- /dev/null
+++ b/scala/qscript/chartl/batchMergePipeline.q
@@ -0,0 +1,39 @@
+import java.io.{FileReader, BufferedReader}
+import org.broadinstitute.sting.datasources.pipeline.Pipeline
+import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK
+import org.broadinstitute.sting.queue.pipeline.{ProjectManagement, BamProcessing, VariantCalling}
+import org.broadinstitute.sting.queue.{QException, QScript}
+import collection.JavaConversions._
+import org.broadinstitute.sting.utils.yaml.YamlUtils
+
+class batchMergePipeline extends QScript {
+  batchMerge =>
+
+  @Argument(doc="VCF list",shortName="vcfs") var vcfList: File = _
+  @Argument(doc="bam list",shortName="bams") var bamList: File = _
+  @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 = _
+
+  def addAll( cmds : List[CommandLineFunction]) : Unit = { cmds.foreach( c => add(c)) }
+
+  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))
+  }
+
+  def extractFileEntries(in: File): List[File] = {
+    var reader : BufferedReader = new BufferedReader(new FileReader(in))
+    var entries : List[File] = Nil
+    var line : String = reader.readLine
+    while ( line != null ) {
+      entries :+= new File(line)
+      line = reader.readLine()
+    }
+
+    return entries
+  }
+}
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diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/ProjectManagement.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/ProjectManagement.scala
new file mode 100755
index 000000000..6cb7f7700
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/ProjectManagement.scala
@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.queue.pipeline
+
+import org.broadinstitute.sting.commandline._
+import org.broadinstitute.sting.queue.util._
+import java.io.File
+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
+
+class ProjectManagement(stingPath: String) {
+
+  pm =>
+
+  var stingDirPath : String = stingPath
+
+  class PassFilterSites(vcf_files: List[File], out_list: File) extends CommandLineFunction {
+    @Input(doc="List of VCFs to extract PF sites from") var vcfs = vcf_files
+    @Output(doc="The file to write the site list to") var out_intervals = out_list
+    @Argument(doc="Path to the SortByRef script") var sortByRef: String = _
+    @Argument(doc="Path to the reference file on disk") var ref: File = _
+
+    def commandLine = {
+      "grep PASS %s | tr ':' '\\t' | awk '{print $2\"\\t\"$3}' | sort -n -k2,2 | uniq | perl %s - %s.fai | awk '{print $1\":\"$2}' > %s".format(
+        vcf_files.foldLeft[String]("")( (b,a) => b + " " + a.getAbsolutePath), sortByRef, ref.getAbsolutePath, out_list.getAbsolutePath
+        )
+    }
+  }
+
+  def MergeBatches( callVCFs: List[File], allBams: List[File], mergedVCF: File, ref: File) : List[CommandLineFunction] = {
+    var cmds : List[CommandLineFunction] = Nil
+    var pfSites : PassFilterSites = new PassFilterSites(callVCFs,swapExt(mergedVCF,".vcf",".pf.intervals.list"))
+    pfSites.sortByRef = pm.stingDirPath+"perl/sortByRef.pl"
+    pfSites.ref = ref
+
+    cmds :+= pfSites
+    
+    var calcs: List[UGCalcLikelihoods] = allBams.map( a => LikelihoodCalc(a,ref,pfSites.out_intervals) )
+
+    cmds ++= calcs
+
+    cmds :+= VariantCallMerge(calcs.map( a => a.out), ref, pfSites.out_intervals, mergedVCF)
+
+    return cmds
+    
+  }
+
+  def LikelihoodCalc( bam: File, ref: File, intervals: File ) : UGCalcLikelihoods = {
+    var calc = new UGCalcLikelihoods
+    calc.input_file :+= bam
+    calc.reference_sequence = ref
+    calc.jarFile = new File(pm.stingDirPath+"dist/GenomeAnalysisTK.jar")
+    calc.intervals :+= intervals
+    calc.downsample_to_coverage = Some(300)
+    calc.memoryLimit = Some(2)
+    calc.min_base_quality_score = Some(22)
+    calc.min_mapping_quality_score = Some(20)
+    calc.genotype = true
+    calc.output_all_callable_bases = true
+    calc.out = swapExt(bam,".bam",".likelihoods.vcf")
+
+    return calc
+  }
+
+  def VariantCallMerge( likelihoods: List[File], ref: File, intervals: File, output: File) : UGCallVariants = {
+    var call = new UGCallVariants
+    call.reference_sequence = ref
+    call.jarFile = new File(pm.stingDirPath+"dist/GenomeAnalysisTK.jar")
+    call.intervals :+= intervals
+    call.memoryLimit = Some(4)
+    call.out = output
+    call.rodBind ++= likelihoods.map( a => new RodBind(a.getName.replace(".vcf",""),"vcf",a) )
+
+    return call
+  }
+
+  def swapExt(file: File, oldExtension: String, newExtension: String) =
+    new File(file.getName.stripSuffix(oldExtension) + newExtension)
+
+}
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