diff --git a/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java b/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java
index 9b51beb53..5f917daa6 100644
--- a/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java
+++ b/java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java
@@ -35,7 +35,8 @@ public class PipelineProject {
     private String name;
     private File referenceFile;
     private File intervalList;
-    private File dbsnpFile;
+    private File genotypeDbsnp;
+    private File evalDbsnp;
     private File refseqTable;
     private Map<String, String> tags = new TreeMap<String, String>();
 
@@ -63,12 +64,40 @@ public class PipelineProject {
         this.referenceFile = referenceFile;
     }
 
+    /** use genotype dbsnp file */
+    @Deprecated
     public File getDbsnpFile() {
-        return dbsnpFile;
+        return getGenotypeDbsnp();
     }
 
+    /** use genotype dbsnp file */
+    @Deprecated
     public void setDbsnpFile(File dbsnpFile) {
-        this.dbsnpFile = dbsnpFile;
+        this.setGenotypeDbsnp(dbsnpFile);
+    }
+
+    public File getGenotypeDbsnp() {
+        return genotypeDbsnp;
+    }
+
+    public void setGenotypeDbsnp(File genotypeDbsnp) {
+        this.genotypeDbsnp = genotypeDbsnp;
+    }
+
+    public String getGenotypeDbsnpType() {
+        return getDbsnpType(genotypeDbsnp);
+    }
+
+    public File getEvalDbsnp() {
+        return evalDbsnp;
+    }
+
+    public void setEvalDbsnp(File evalDbsnp) {
+        this.evalDbsnp = evalDbsnp;
+    }
+
+    public String getEvalDbsnpType() {
+        return getDbsnpType(genotypeDbsnp);
     }
 
     public File getRefseqTable() {
@@ -86,4 +115,13 @@ public class PipelineProject {
     public void setTags(Map<String, String> tags) {
         this.tags = tags;
     }
+
+    private String getDbsnpType(File file) {
+        if (file == null)
+            return null;
+        else if (file.getName().toLowerCase().endsWith(".vcf"))
+            return "vcf";
+        else
+            return "dbsnp";
+    }
 }
diff --git a/scala/qscript/playground/fullCallingPipeline.q b/scala/qscript/playground/FullCallingPipeline.q
similarity index 94%
rename from scala/qscript/playground/fullCallingPipeline.q
rename to scala/qscript/playground/FullCallingPipeline.q
index 487e2fe5a..095463a25 100755
--- a/scala/qscript/playground/fullCallingPipeline.q
+++ b/scala/qscript/playground/FullCallingPipeline.q
@@ -10,7 +10,7 @@ import org.broadinstitute.sting.queue.QScript
 import collection.JavaConversions._
 import org.broadinstitute.sting.utils.yaml.YamlUtils
 
-class fullCallingPipeline extends QScript {
+class FullCallingPipeline extends QScript {
   qscript =>
 
   @Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
@@ -64,8 +64,6 @@ class fullCallingPipeline extends QScript {
 
   private var pipeline: Pipeline = _
 
-  private var dbsnpType: String = _
-
   trait CommandLineGATKArgs extends CommandLineGATK {
     this.intervals = List(qscript.pipeline.getProject.getIntervalList)
     this.jarFile = qscript.gatkJar
@@ -79,12 +77,6 @@ class fullCallingPipeline extends QScript {
 
   def script = {
     pipeline = YamlUtils.load(classOf[Pipeline], qscript.yamlFile)
-    //var dbsnpType: String = _ //figure out how to get it so this is recognized and the whole thing has access to it.
-      if (qscript.pipeline.getProject.getDbsnpFile.toString.contains("rod")){
-        dbsnpType = "dbSNP"
-      } else  {
-        dbsnpType = "VCF"
-      }
 
     val projectBase: String = qscript.pipeline.getProject.getName
     // TODO: Fix command lines that pass -refseqTable
@@ -131,7 +123,7 @@ class fullCallingPipeline extends QScript {
         realigner.intervals = Nil
         realigner.intervalsString = Nil
         realigner.scatterCount = num_cleaner_scatter_jobs
-        realigner.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
+        realigner.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
         realigner.rodBind :+= RodBind("indels", "VCF", swapExt(realigner.reference_sequence.getParentFile, realigner.reference_sequence, "fasta", "1kg_pilot_indels.vcf"))
 
         // if scatter count is > 1, do standard scatter gather, if not, explicitly set up fix mates
@@ -214,7 +206,7 @@ class fullCallingPipeline extends QScript {
     snps.group :+= "Standard"
     snps.out = new File("SnpCalls", base+".vcf")
     snps.downsample_to_coverage = Some(qscript.downsampling_coverage)
-    snps.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
+    snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
     snps.memoryLimit = Some(6)
 
     snps.scatterCount = qscript.num_snp_scatter_jobs
@@ -242,7 +234,7 @@ class fullCallingPipeline extends QScript {
     indels.group :+= "Standard"
     indels.out = new File("IndelCalls", base+".vcf")
     indels.downsample_to_coverage = Some(qscript.downsampling_coverage)
-    indels.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
+    indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
     indels.memoryLimit = Some(6)
     indels.genotype_likelihoods_model = Option(org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL)
 
@@ -308,12 +300,7 @@ class fullCallingPipeline extends QScript {
     eval.reportLocation = new File("SnpCalls", base+".eval")
     eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R)
     eval.analysisName = base+"_VariantEval"
-    if(dbsnpType=="VCF"){
-     eval.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_b37.rod")
-
-    } else{
-      eval.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
-    }
+    eval.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getEvalDbsnpType, qscript.pipeline.getProject.getEvalDbsnp)
 
     // 5. Make the bam list
     val listOfBams =  new File(base +".BamFiles.list")
diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
index 6e2177d02..96cea668a 100644
--- a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
+++ b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala
@@ -23,11 +23,6 @@ class FullCallingPipelineTest {
     new K1gBam("C474", "NA19652", 1),
     new K1gBam("C474", "NA19654", 1))
 
-  // In fullCallingPipeline.q VariantEval is always compared against 129.
-  // Until the newvarianteval is finalized which will allow java import of the prior results,
-  // we re-run VariantEval to validate the run, and replicate that behavior here.
-  private final val variantEvalDbsnpFile = new File(BaseTest.b37dbSNP129)
-
   val k1gChr20Dataset = {
     val dataset = newK1gDataset("Barcoded_1000G_WEx_chr20")
     dataset.pipeline.getProject.setIntervalList(new File(BaseTest.GATKDataLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list"))
@@ -64,7 +59,8 @@ class FullCallingPipelineTest {
     val project = new PipelineProject
     project.setName(projectName)
     project.setReferenceFile(new File(BaseTest.hg19Reference))
-    project.setDbsnpFile(new File(BaseTest.b37dbSNP132))
+    project.setGenotypeDbsnp(new File(BaseTest.b37dbSNP132))
+    project.setEvalDbsnp(new File(BaseTest.b37dbSNP129))
     project.setRefseqTable(new File(BaseTest.hg19Refseq))
 
     var samples = List.empty[PipelineSample]
@@ -94,12 +90,12 @@ class FullCallingPipelineTest {
   @Test(dataProvider="datasets", enabled=false)
   def testFullCallingPipeline(dataset: PipelineDataset) = {
     val projectName = dataset.pipeline.getProject.getName
-    val testName = "fullCallingPipeline-" + projectName
+    val testName = "FullCallingPipeline-" + projectName
     val yamlFile = writeYaml(testName, dataset.pipeline)
     var cleanType = "cleaned"
 
     // Run the pipeline with the expected inputs.
-    var pipelineCommand = ("-retry 1 -S scala/qscript/playground/fullCallingPipeline.q" +
+    var pipelineCommand = ("-retry 1 -S scala/qscript/playground/FullCallingPipeline.q" +
             " -jobProject %s -Y %s" +
             " -tearScript %s/R/DataProcessingReport/GetTearsheetStats.R" +
             " --gatkjar %s")
@@ -119,7 +115,7 @@ class FullCallingPipelineTest {
     pipelineSpec.evalSpec.vcf = new File(PipelineTest.runDir(testName) + "SnpCalls/%s.%s.annotated.handfiltered.vcf".format(projectName, cleanType))
     pipelineSpec.evalSpec.reference = dataset.pipeline.getProject.getReferenceFile
     pipelineSpec.evalSpec.intervals = dataset.pipeline.getProject.getIntervalList
-    pipelineSpec.evalSpec.dbsnp = variantEvalDbsnpFile
+    pipelineSpec.evalSpec.dbsnp = dataset.pipeline.getProject.getEvalDbsnp
     pipelineSpec.evalSpec.validations = dataset.validations
 
     // Run the test, at least checking if the command compiles
diff --git a/shell/getFirehosePipelineYaml.sh b/shell/getFirehosePipelineYaml.sh
index a6e1ef10c..8f03b1e4b 100755
--- a/shell/getFirehosePipelineYaml.sh
+++ b/shell/getFirehosePipelineYaml.sh
@@ -32,19 +32,22 @@ FIREHOSE_ANNOTATIONS=(reference_file interval_list \
 
 # YAML templates
 
+# Project YAML template, once per file.
 PROJECT_YAML_TEMPLATE='"\n\
   project: {\n\
     name: '"$ENTITY_SET_ID"',\n\
     referenceFile: %s,\n\
-    dbsnpFile: %s,\n\
+    genotypeDbsnpFile: %s,\n\
+    evalDbsnpFile: %s,\n\
     refseqTable: %s,\n\
     intervalList: %s\n\
-  },", $1, dbsnp, refseq, $2'
+  },", $1, genotypeDbsnp, evalDbsnp, refseq, $2'
 
+# Project YAML template, once per sample.
 SAMPLE_YAML_TEMPLATE='"\n\
     {\n\
       id: %s,\n\
-      bamFiles: { recalibrated: %s },\n\
+      bamFiles: { cleaned: %s },\n\
       tags: {\n\
         SQUIDProject: %s,\n\
         CollaboratorID: %s\n\
@@ -86,20 +89,27 @@ BEGIN {
     refseq_dir = "/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/";
     dbsnp_dir = "/humgen/gsa-hpprojects/GATK/data/";
 
-    dbsnps["Homo_sapiens_assembly18.fasta"] = dbsnp_dir "dbsnp_129_hg18.rod";
+    # add hg18 specific files to awk associative arrays
+    genotypeDbsnps["Homo_sapiens_assembly18.fasta"] = dbsnp_dir "dbsnp_129_hg18.rod";
+    evalDbsnps["Homo_sapiens_assembly18.fasta"] = dbsnp_dir "dbsnp_129_hg18.rod";
     refseqs["Homo_sapiens_assembly18.fasta"] = refseq_dir "refGene-big-table-hg18.txt";
 
-    dbsnps["Homo_sapiens_assembly19.fasta"] = dbsnp_dir "dbsnp_132_b37.vcf";
+    # add hg19 specific files to awk associative arrays
+    genotypeDbsnps["Homo_sapiens_assembly19.fasta"] = dbsnp_dir "dbsnp_132_b37.vcf";
+    evalDbsnps["Homo_sapiens_assembly19.fasta"] = dbsnp_dir "dbsnp_129_b37.rod";
     refseqs["Homo_sapiens_assembly19.fasta"] = refseq_dir "refGene-big-table-hg19.txt";
 
     printf "{"
 }
 {
     if (NR == 1) {
+        # Based on the reference of the first sample, specify the dbsnps and refseq tables.
+
         reference_part_count = split($1, reference_parts, "/")
         reference_name = reference_parts[reference_part_count];
 
-        dbsnp = dbsnps[reference_name];
+        genotypeDbsnp = genotypeDbsnps[reference_name];
+        evalDbsnp = evalDbsnps[reference_name];
         refseq = refseqs[reference_name];
 
         printf '"$PROJECT_YAML_TEMPLATE"'
@@ -115,12 +125,14 @@ END {
     print "\n}"
 }' > $PIPELINE_YAML_FILE
 
-hg19=`grep "assembly19" -c $PIPELINE_YAML_FILE`
+#hg19=`grep "assembly19" -c $PIPELINE_YAML_FILE`
 
-if [ "$hg19" -ne 0 ]; then
-    sed 's/\/humgen.*rod/\/humgen\/gsa-hpprojects\/GATK\/data\/dbsnp_132_b37.vcf/' $PIPELINE_YAML_FILE > yaml2 
-    mv yaml2 $PIPELINE_YAML_FILE
-fi
+# NOTE: DBSNP's are populated via AWK's BEGIN block above.
+#if [ "$hg19" -ne 0 ]; then
+#    sed 's/\/humgen.*rod/\/humgen\/gsa-hpprojects\/GATK\/data\/dbsnp_132_b37.vcf/' $PIPELINE_YAML_FILE > yaml2
+#    mv yaml2 $PIPELINE_YAML_FILE
+#fi
 
-sed 's/recalibrat/clean/' $PIPELINE_YAML_FILE > yaml2
-mv yaml2 $PIPELINE_YAML_FILE
+# NOTE: Renamed "recalibrated" to "cleaned" in SAMPLE_YAML_TEMPLATE above.
+#sed 's/recalibrat/clean/' $PIPELINE_YAML_FILE > yaml2
+#mv yaml2 $PIPELINE_YAML_FILE
diff --git a/shell/queue.sh b/shell/queue.sh
index a939f5525..3b2826d92 100755
--- a/shell/queue.sh
+++ b/shell/queue.sh
@@ -2,7 +2,6 @@
 
 SAMPLE_SET=$1
 STING_HOME=/humgen/gsa-pipeline/.repository
-REFSEQ_TABLE=/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/refGene-big-table-hg19.txt
 JOB_QUEUE=week
 SHORT_QUEUE=hour
 TMP_DIR=$PWD/tmp
@@ -14,4 +13,4 @@ use R-2.10
 use Oracle-full-client
 use .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
 
-java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript "$STING_HOME"/R/DataProcessingReport/GetTearsheetStats.R -S "$STING_HOME"/scala/qscript/playground/fullCallingPipeline.q -Y "$SAMPLE_SET".yaml -refseqTable "$REFSEQ_TABLE" --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2
+java -Djava.io.tmpdir="$TMP_DIR" -jar "$STING_HOME"/dist/Queue.jar -jobQueue "$JOB_QUEUE" -shortJobQueue "$SHORT_QUEUE" -jobProject "$SAMPLE_SET" -jobPrefix "$SAMPLE_SET" -tearScript "$STING_HOME"/R/DataProcessingReport/GetTearsheetStats.R -S "$STING_HOME"/scala/qscript/playground/FullCallingPipeline.q -Y "$SAMPLE_SET".yaml --gatkjar "$STING_HOME"/dist/GenomeAnalysisTK.jar -log queue_log.txt -statusTo corin -bsub $2