diff --git a/scala/qscript/chartl/fullCallingPipelineV2.q b/scala/qscript/chartl/fullCallingPipelineV2.q
index 2c3976d70..0f0efe01c 100755
--- a/scala/qscript/chartl/fullCallingPipelineV2.q
+++ b/scala/qscript/chartl/fullCallingPipelineV2.q
@@ -1,79 +1,31 @@
+import org.broadinstitute.sting.commandline.ArgumentCollection
 import org.broadinstitute.sting.datasources.pipeline.Pipeline
 import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK
-import org.broadinstitute.sting.queue.pipeline.{BamProcessing,VariantCalling}
+import org.broadinstitute.sting.queue.pipeline._
+import org.broadinstitute.sting.queue.util.PipelineUtils
 import org.broadinstitute.sting.queue.{QException, QScript}
 import collection.JavaConversions._
 import org.broadinstitute.sting.utils.yaml.YamlUtils
 
 class fullCallingPipelineV2 extends QScript {
-  qscript =>
-
-  @Argument(doc="Number of cleaning jobs", shortName="cleaningJobs", required=false)
-  var cleaningJobs: Int = 1
-
-  @Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
-  var yamlFile: File = _
-
-  @Input(doc="path to trigger track (for UnifiedGenotyper)", shortName="trigger", required=false)
-  var trigger: File = _
-
-  @Input(doc="path to refseqTable (for GenomicAnnotator)", shortName="refseqTable")
-  var refseqTable: File = _
-
-  @Input(doc="path to Picard FixMateInformation.jar.  See http://picard.sourceforge.net/ .", required=false)
-  var picardFixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
-
-  @Input(doc="path to GATK jar", shortName="gatk")
-  var gatkJar: File = _
-
-  @Input(doc="target Ti/Tv ratio for recalibration", shortName="titv", required=true)
-  var target_titv: Float = _
-
-  @Input(doc="per-sample downsampling level",shortName="dcov",required=false)
-  var downsampling_coverage = 300
-
-  @Input(doc="level of parallelism for UnifiedGenotyper", shortName="snpScatter", required=false)
-  var num_snp_scatter_jobs = 20
-
-  @Input(doc="level of parallelism for IndelGenotyperV2", shortName="indelScatter", required=false)
-  var num_indel_scatter_jobs = 5
-
-  @Input(doc="Skip indel-cleaning for BAM files (for testing only)", shortName="skipCleaning", required=false)
-  var skip_cleaning = false
-
-  //@Input(doc="ADPR script")
-  //var adprScript: File = _
-
-  //@Input(doc="Sequencing maching name (for use by adpr)")
-  //var machine: String = _
-
-  //@Input(doc="Sequencing experiement type (for use by adpr)--Whole_Exome, Whole_Genome, or Hybrid_Selection")
-  //var protocol: String = _
+  fcp =>
 
+  @ArgumentCollection var pipelineArgs = new PipelineArgumentCollection
+  
   private var pipeline: Pipeline = _
 
-  trait CommandLineGATKArgs extends CommandLineGATK {
-    this.intervals :+= qscript.pipeline.getProject.getIntervalList
-    this.jarFile = qscript.gatkJar
-    this.reference_sequence = qscript.pipeline.getProject.getReferenceFile
-    this.memoryLimit = Some(4)
-  }
-
-
-  // ------------ SETUP THE PIPELINE ----------- //
-
-
   def script = {
-    pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile)
-    var callingLib: VariantCalling = new VariantCalling(qscript.yamlFile,qscript.gatkJar)
-    var cleaningLib: BamProcessing = new BamProcessing(qscript.yamlFile,qscript.gatkJar,qscript.picardFixMatesJar)
+    pipelineArgs.verifyArguments
+    pipeline = PipelineUtils.loadPipelineFromPAC(pipelineArgs)
+    var callingLib: VariantCalling = new VariantCalling(pipeline,fcp.pipelineArgs.gatkJar)
+    var cleaningLib: BamProcessing = new BamProcessing(pipeline,fcp.pipelineArgs.gatkJar,fcp.pipelineArgs.picardFixMatesJar)
 
-    val projectBase: String = qscript.pipeline.getProject.getName
+    val projectBase: String = fcp.pipeline.getProject.getName
     val cleanedBase: String = projectBase + ".cleaned"
     val uncleanedBase: String = projectBase + ".uncleaned"
 
     // there are commands that use all the bam files
-    val recalibratedSamples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains("recalibrated"))
+    val recalibratedSamples = fcp.pipeline.getSamples.filter( u => ( u.getBamFiles.contains("recalibrated") || u.getBamFiles.contains("cleaned") ) )
 
     var bamsToClean: List[(File,File)] = Nil
     var recalBams: List[File] = Nil
@@ -90,11 +42,11 @@ class fullCallingPipelineV2 extends QScript {
       cleanedBams :+= sample.getBamFiles.get("cleaned")
     }
 
-    if ( !qscript.skip_cleaning ) {
-      addAll(cleaningLib.StandardIndelRealign(bamsToClean,qscript.cleaningJobs))
+    if ( !fcp.pipelineArgs.skip_cleaning ) {
+      addAll(cleaningLib.StandardIndelRealign(bamsToClean,fcp.pipelineArgs.cleaningJobs))
     }
 
-    if (!qscript.skip_cleaning) {
+    if (!fcp.pipelineArgs.skip_cleaning ) {
       endToEnd(cleanedBase, cleanedBams, callingLib)
     } else {
       endToEnd(uncleanedBase, recalBams, callingLib)
@@ -107,12 +59,8 @@ class fullCallingPipelineV2 extends QScript {
     var handfilt_vcf = new File(base+"_snps.handfiltered.annotated.vcf")
     var indel_vcf = new File(base+"_indel_calls.vcf")
 
-    addAll(lib.StandardCallingPipeline(bamFiles,indel_vcf,recal_vcf,handfilt_vcf,qscript.target_titv,qscript.refseqTable))
+    addAll(lib.StandardCallingPipeline(bamFiles,indel_vcf,recal_vcf,handfilt_vcf,fcp.pipelineArgs.target_titv,fcp.pipelineArgs.refseqTable))
   }
 
-  def addAll(clfs: List[CommandLineFunction]) = {
-    for ( c <- clfs ) {
-      add(c)
-    }
-  }
+  def addAll(clfs: List[CommandLineFunction]) = { clfs.foreach(c => add(c)) }
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala
index cbf9f9356..74cfd05f2 100755
--- a/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala
@@ -16,10 +16,13 @@ import org.broadinstitute.sting.queue.util.{PipelineUtils, IOUtils}
 import org.broadinstitute.sting.commandline.{Output, Input}
 import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
 
-class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
+class BamProcessing(attribs: Pipeline, gatkJar: File, fixMatesJar: File) {
   library =>
 
-  var attributes: Pipeline = YamlUtils.load(classOf[Pipeline],yaml)
+  var attributes : Pipeline = attribs
+
+  def this(yaml: File, gatkJar: File, fixMatesJar: File) = this(YamlUtils.load(classOf[Pipeline],yaml),gatkJar,fixMatesJar)
+
 
   trait StandardCommandLineGATK extends CommandLineGATK {
     this.reference_sequence = library.attributes.getProject.getReferenceFile
diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/PipelineArgumentCollection.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/PipelineArgumentCollection.scala
new file mode 100755
index 000000000..e7c741cef
--- /dev/null
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/PipelineArgumentCollection.scala
@@ -0,0 +1,86 @@
+package org.broadinstitute.sting.queue.pipeline
+
+import org.broadinstitute.sting.commandline.{Input, Argument, Hidden}
+import java.io.File
+
+
+class PipelineArgumentCollection {
+
+  @Argument(doc="Number of cleaning jobs", shortName="cleaningJobs", required=false)
+  var cleaningJobs: Int = 1
+
+  @Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y", required=false)
+  var yamlFile: File = _
+
+  @Input(doc="path to trigger track (for UnifiedGenotyper)", shortName="trigger", required=false)
+  var trigger: File = _
+
+  @Input(doc="path to refseqTable (for GenomicAnnotator)", shortName="refseqTable")
+  var refseqTable: File = _
+
+  @Input(doc="path to Picard FixMateInformation.jar.  See http://picard.sourceforge.net/ .", required=false)
+  var picardFixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
+
+  @Input(doc="path to GATK jar", shortName="gatk")
+  var gatkJar: File = _
+
+  @Input(doc="target Ti/Tv ratio for recalibration", shortName="titv", required=true)
+  var target_titv: Float = _
+
+  @Input(doc="per-sample downsampling level",shortName="dcov",required=false)
+  var downsampling_coverage = 300
+
+  @Input(doc="level of parallelism for UnifiedGenotyper", shortName="snpScatter", required=false)
+  var num_snp_scatter_jobs = 20
+
+  @Input(doc="level of parallelism for IndelGenotyperV2", shortName="indelScatter", required=false)
+  var num_indel_scatter_jobs = 5
+
+  @Input(doc="Skip indel-cleaning for BAM files (for testing only)", shortName="skipCleaning", required=false)
+  var skip_cleaning = false
+
+  @Input(doc="List of samples and bams (in the form sample_id k1:v1,k2:v2 "+
+          "cleaned:/path/to/cleaned.bam,recalibrated:/path/to/recal.bam,unreacalibrated:/path/to/unrecal.bam)."+
+          "Mutually exclusive with YAML",required=false, shortName="pBams")
+  var projectBams: File = _
+
+  @Input(doc="The project name. Mutually exclusive with YAML.", required = false, shortName="pName")
+  var projectName: String = _
+
+  @Input(doc="The reference file. Mutually exclusive with YAML.", required=false, shortName="pRef")
+  var projectRef: File = _
+
+  @Input(doc="The project interval list. Mutually exclusive with YAML.", required=false, shortName="pInt")
+  var projectIntervals: File = _
+
+  @Input(doc="The project dbsnp. Mutually exclusive with YAML",required=false, shortName="pDB")
+  var projectDBSNP: File = _
+
+  //@Input(doc="ADPR script")
+  //var adprScript: File = _
+
+  //@Input(doc="Sequencing maching name (for use by adpr)")
+  //var machine: String = _
+
+  //@Input(doc="Sequencing experiement type (for use by adpr)--Whole_Exome, Whole_Genome, or Hybrid_Selection")
+  //var protocol: String = _
+
+  def verifyArguments = {
+    // if no yaml file we require all the mutually exclusive arguments
+    if ( yamlFile == null ) {
+      if ( projectBams == null ) throw new IllegalArgumentException("No YAML file provided; and no project bam list. Pipeline requires either YAML file, or full project specs.")
+
+      if ( projectName == null ) throw new IllegalArgumentException("No YAML file provided; and no project name. Pipeline requires either YAML file, or full project specs.")
+
+      if ( projectRef == null) throw new IllegalArgumentException("No YAML file provided; and no project reference. Pipeline requires either YAML file, or full project specs.")
+
+      if ( projectIntervals == null ) throw new IllegalArgumentException("No YAML file provided; and no project intervals. Pipeline requires either YAML file, or full project specs.")
+
+      if ( projectDBSNP == null ) throw new IllegalArgumentException("No YAML file provided; and no project DBSNP. Pipeline requires either YAML file, or full project specs.")
+    } else {
+      if ( projectBams != null || projectName != null || projectRef != null || projectIntervals != null || projectDBSNP != null )
+        throw new IllegalArgumentException("YAML file provided, along with other project spec arguments. YAML file is mutually exclusive with project specs.")
+    }
+  }
+
+}
\ No newline at end of file
diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/ProjectManagement.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/ProjectManagement.scala
index 8f3e30f0b..c255819b2 100755
--- a/scala/src/org/broadinstitute/sting/queue/pipeline/ProjectManagement.scala
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/ProjectManagement.scala
@@ -15,22 +15,22 @@ class ProjectManagement(stingPath: String) {
 
   var stingDirPath : String = stingPath
 
-  class PassFilterSites(vcf_files: List[File], out_list: File) extends CommandLineFunction {
+  class PassFilterAlleles(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
+      "egrep \"FORMAT|format\" %s | cut -f1-8 > %s ; grep PASS %s | tr ':' '\\t' | awk '{print $2\"\\t\"$3\"\\t\"$4\"\\t\"$5\"\\t\"$6\"\\t.\\t.\\t.\"}' | sort -n -k2,2 | uniq | perl %s - %s.fai >> %s".format(
+        vcf_files(1).getAbsolutePath, out_list.getAbsolutePath, 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"))
+    var pfSites : PassFilterAlleles = new PassFilterAlleles(callVCFs,swapExt(mergedVCF,".vcf",".pf.alleles.vcf"))
     pfSites.sortByRef = pm.stingDirPath+"perl/sortByRef.pl"
     pfSites.ref = ref
 
@@ -46,12 +46,11 @@ class ProjectManagement(stingPath: String) {
     
   }
 
-  def LikelihoodCalc( bam: File, ref: File, intervals: File ) : UGCalcLikelihoods = {
+  def LikelihoodCalc( bam: File, ref: File, alleleVCF: 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)
@@ -59,15 +58,18 @@ class ProjectManagement(stingPath: String) {
     calc.genotype = true
     calc.output_all_callable_bases = true
     calc.out = swapExt(bam,".bam",".likelihoods.vcf")
+    calc.rodBind :+= new RodBind("allele","VCF",alleleVCF)
+    calc.BTI = "allele"
 
     return calc
   }
 
-  def VariantCallMerge( likelihoods: List[File], ref: File, intervals: File, output: File) : UGCallVariants = {
+  def VariantCallMerge( likelihoods: List[File], ref: File, intervalVCF: 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.rodBind :+= new RodBind("allele","vcf",intervalVCF)
+    call.BTI = "allele"
     call.memoryLimit = Some(4)
     call.out = output
     call.rodBind ++= likelihoods.map( a => new RodBind("variant"+a.getName.replace(".vcf",""),"vcf",a) )
diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
index 024ecfd3f..3983e3538 100755
--- a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
+++ b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
@@ -8,12 +8,14 @@ import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.utils.yaml.YamlUtils
 import org.broadinstitute.sting.queue.function.CommandLineFunction
 
-class VariantCalling(yaml: File,gatkJar: File) {
+class VariantCalling(attribs: Pipeline,gatkJar: File) {
   vc =>
 
   // load attributes
-  var attributes: Pipeline = YamlUtils.load(classOf[Pipeline], yaml)
-  
+  var attributes = attribs
+
+  def this(yaml: File, gatkJar: File) = this(YamlUtils.load(classOf[Pipeline],yaml),gatkJar)
+
   /**
    * Trait to propagate basic attributes throughout the library
    */
diff --git a/scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala b/scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala
index 19c34071e..ec6aa28d7 100755
--- a/scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala
+++ b/scala/src/org/broadinstitute/sting/queue/util/PipelineUtils.scala
@@ -5,6 +5,10 @@ import java.io.File
 import org.broadinstitute.sting.utils.GenomeLocParser
 import collection.JavaConversions._
 import org.broadinstitute.sting.utils.interval.IntervalUtils
+import org.broadinstitute.sting.queue.pipeline.PipelineArgumentCollection
+import org.broadinstitute.sting.utils.yaml.YamlUtils
+import org.broadinstitute.sting.datasources.pipeline.{PipelineSample, PipelineProject, Pipeline}
+import org.broadinstitute.sting.utils.text.XReadLines
 
 class PipelineUtils {
 
@@ -52,4 +56,46 @@ object PipelineUtils{
 
     splitContigs.map{case (size, contigs) => contigs}
   }
+
+  def loadPipelineFromPAC(args: PipelineArgumentCollection) : Pipeline = {
+    if ( args.yamlFile != null ) {
+      return YamlUtils.load(classOf[Pipeline], args.yamlFile)
+    } else {
+      return loadPipelineFromSpec(args.projectName,args.projectRef,args.projectIntervals,args.projectDBSNP,args.projectBams)
+    }
+  }
+
+  def loadPipelineFromSpec(name: String, ref: File, ivals: File, dbsnp: File, pBamList: File) : Pipeline = {
+    var newPipeline : Pipeline = new Pipeline
+    var pipeProject : PipelineProject = new PipelineProject
+    var pipeSamples : List[PipelineSample] = ((new XReadLines(pBamList)).readLines).toList.map( bamSpecToSample )
+
+    pipeProject.setName(name)
+    pipeProject.setReferenceFile(ref)
+    pipeProject.setIntervalList(ivals)
+    pipeProject.setDbsnpFile(dbsnp)
+
+    newPipeline.setProject(pipeProject)
+    newPipeline.setSamples(pipeSamples)
+    
+    return newPipeline
+  }
+
+  //todo -- find a better name for this function
+  def bamSpecToSample(spec: String) : PipelineSample = {
+    var sam : PipelineSample = new PipelineSample
+    var spStr : Array[String] = spec.split("\\s")
+    sam.setId(spStr(0))
+    var tagStr : Array[String] = spStr(1).split(",")
+    var tagMap : java.util.HashMap[String,String] = new java.util.HashMap[String,String](tagStr.size)
+    tagStr.filter( u => ! u.equals("")).foreach( u => tagMap.put(u.split(":")(0),u.split(":")(1)) )
+    sam.setTags(tagMap)
+    var bamStr : Array[String] = spStr(2).split(",")
+    var bamMap : java.util.HashMap[String,File] = new java.util.HashMap[String,File](bamStr.size)
+    bamStr.foreach( u => bamMap.put( u.split(":")(0), new File(u.split(":")(1) ) ) )
+    sam.setBamFiles(bamMap)
+
+    return sam
+
+  }
 }
\ No newline at end of file