diff --git a/R/plot_Tranches.R b/R/plot_Tranches.R
index 075375340..0b0152de3 100755
--- a/R/plot_Tranches.R
+++ b/R/plot_Tranches.R
@@ -52,7 +52,7 @@ alpha = 1 - titvFPEstV(targetTITV, novelTiTv)
 
 numGood = round(alpha * data2$numNovel);
 
-#numGood = round(data2$numNovel * (1-data2$FDRtranche/100))
+#numGood = round(data2$numNovel * (1-data2$targetTruthSensitivity/100))
 numBad = data2$numNovel - numGood;
 
 numPrevGood = leftShift(numGood, 0)
@@ -66,12 +66,12 @@ barplot(d/1000,horiz=TRUE,col=cols,space=0.2,xlab="Number of Novel Variants (100
 #abline(v= d[2,dim(d)[2]], lty=2)
 #abline(v= d[1,3], lty=2)
 if ( ! suppressLegend ) 
-    legend(5, 1.75, c('Cumulative TPs','Tranch-specific TPs', 'Tranch-specific FPs', 'Cumulative FPs' ), fill=cols, density=density, bg='white', cex=1.25)
+    legend(5, length(data2$targetTruthSensitivity)-1.25, c('Cumulative TPs','Tranch-specific TPs', 'Tranch-specific FPs', 'Cumulative FPs' ), fill=cols, density=density, bg='white', cex=1.25)
 
-mtext("Ti/Tv",2,line=2.25,at=length(data2$FDRtranche)*1.2,las=1, cex=1)
-mtext("FNR",2,line=0,at=length(data2$FDRtranche)*1.2,las=1, cex=1)
-axis(2,line=-1,at=0.7+(0:(length(data2$FDRtranche)-1))*1.2,tick=FALSE,labels=data2$FDRtranche, las=1, cex.axis=1.0)
-axis(2,line=1,at=0.7+(0:(length(data2$FDRtranche)-1))*1.2,tick=FALSE,labels=round(novelTiTv,3), las=1, cex.axis=1.0)
+mtext("Ti/Tv",2,line=2.25,at=length(data2$targetTruthSensitivity)*1.2,las=1, cex=1)
+mtext("truth",2,line=0,at=length(data2$targetTruthSensitivity)*1.2,las=1, cex=1)
+axis(2,line=-1,at=0.7+(0:(length(data2$targetTruthSensitivity)-1))*1.2,tick=FALSE,labels=data2$targetTruthSensitivity, las=1, cex.axis=1.0)
+axis(2,line=1,at=0.7+(0:(length(data2$targetTruthSensitivity)-1))*1.2,tick=FALSE,labels=round(novelTiTv,3), las=1, cex.axis=1.0)
 
 # plot sensitivity vs. specificity
 sensitivity = data2$truthSensitivity
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 4250866f1..631453656 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -43,6 +43,7 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.util.*;
@@ -68,11 +69,13 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     @Output(fullName="recal_file", shortName="recalFile", doc="The output recal file used by ApplyRecalibration", required=true)
     private PrintStream RECAL_FILE;
     @Output(fullName="tranches_file", shortName="tranchesFile", doc="The output tranches file used by ApplyRecalibration", required=true)
-    private PrintStream TRANCHES_FILE;
+    private File TRANCHES_FILE;
 
     /////////////////////////////
     // Additional Command Line Arguments
     /////////////////////////////
+    @Argument(fullName="target_titv", shortName="titv", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!", required=false)
+    private double TARGET_TITV = 2.15;
     @Argument(fullName="use_annotation", shortName="an", doc="The names of the annotations which should used for calculations", required=true)
     private String[] USE_ANNOTATIONS = null;
     @Argument(fullName="TStranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false)
@@ -83,6 +86,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     private String PATH_TO_RSCRIPT = "Rscript";
     @Argument(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false)
     private String RSCRIPT_FILE = null;
+    @Argument(fullName = "path_to_resources", shortName = "resources", doc = "Path to resources folder holding the Sting R scripts.", required=false)
+    private String PATH_TO_RESOURCES = "R/";
     @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots", required=false)
     private double TS_FILTER_LEVEL = 99.0;
 
@@ -97,6 +102,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     // Private Member Variables
     /////////////////////////////
     private VariantDataManager dataManager;
+    private PrintStream tranchesStream;
     private final Set<String> ignoreInputFilterSet = new TreeSet<String>();
     private final Set<String> inputNames = new HashSet<String>();
     private final VariantRecalibratorEngine engine = new VariantRecalibratorEngine( VRAC );
@@ -136,6 +142,12 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         if( inputNames.size() == 0 ) {
             throw new UserException.BadInput( "No input variant tracks found. Input variant binding names must begin with 'input'." );
         }
+
+        try {
+            tranchesStream = new PrintStream(TRANCHES_FILE);
+        } catch (FileNotFoundException e) {
+            throw new UserException.CouldNotCreateOutputFile(TRANCHES_FILE, e);
+        }
     }
 
     //---------------------------------------------------------------------------------------------------------------
@@ -224,7 +236,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         final int nCallsAtTruth = TrancheManager.countCallsAtTruth( dataManager.getData(), Double.NEGATIVE_INFINITY );
         final TrancheManager.SelectionMetric metric = new TrancheManager.TruthSensitivityMetric( nCallsAtTruth );
         final List<Tranche> tranches = TrancheManager.findTranches( dataManager.getData(), TS_TRANCHES, metric );
-        TRANCHES_FILE.print(Tranche.tranchesString( tranches ));
+        tranchesStream.print(Tranche.tranchesString( tranches ));
 
         double lodCutoff = 0.0;
         for( final Tranche tranche : tranches ) {
@@ -240,6 +252,20 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             createVisualizationScript( randomData, goodModel, badModel, lodCutoff );
         }
 
+        // Execute Rscript command to create the tranche plot
+        // Print out the command line to make it clear to the user what is being executed and how one might modify it
+        final String rScriptTranchesCommandLine = PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Tranches.R" + " " + TRANCHES_FILE.getAbsolutePath() + " " + TARGET_TITV;
+        logger.info( rScriptTranchesCommandLine );
+
+        // Execute the RScript command to plot the table of truth values
+        try {
+            Process p;
+            p = Runtime.getRuntime().exec( rScriptTranchesCommandLine );
+            p.waitFor();
+        } catch ( Exception e ) {
+            Utils.warnUser("Unable to execute the RScript command.  While not critical to the calculations themselves, the script outputs a report that is extremely useful for confirming that the recalibration proceded as expected.  We highly recommend trying to rerun the script manually if possible.");
+        }
+
     }
 
     private void createVisualizationScript( final ExpandingArrayList<VariantDatum> randomData, final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel, final double lodCutoff ) {