diff --git a/R/plot_Annotations_BinnedTiTv.R b/R/plot_Annotations_BinnedTiTv.R
index 89c5f1c69..88e9597a3 100644
--- a/R/plot_Annotations_BinnedTiTv.R
+++ b/R/plot_Annotations_BinnedTiTv.R
@@ -28,7 +28,8 @@ xmax = max(d$value)
 outfile = paste(outputDir, "binnedTiTv.", annotationName, ".pdf", sep="")
 pdf(outfile, height=7, width=7)
 par(cex=1.1)
-plot(all$value,all$titv,xlab=annotationName,ylab="Ti/Tv ratio",pch=20,ylim=c(ymin,ymax));
+plot(all$value,all$titv,xlab=annotationName,ylab="Ti/Tv ratio",pch=20,ylim=c(ymin,ymax),xaxt="n");
+axis(1,axTicks(1), format(axTicks(1), scientific=F))
 m = weighted.mean(all$value,all$numVariants/sum(all$numVariants))
 ma = all[all$value > m,]
 mb = all[all$value < m,]
@@ -45,7 +46,8 @@ dev.off()
 outfile = paste(outputDir, "binnedTiTv_log.", annotationName, ".pdf", sep="")
 pdf(outfile, height=7, width=7)
 par(cex=1.1)
-plot(all$value,all$titv,xlab=annotationName,log="x",ylab="Ti/Tv ratio",pch=20,ylim=c(ymin,ymax));
+plot(all$value,all$titv,xlab=annotationName,log="x",ylab="Ti/Tv ratio",pch=20,ylim=c(ymin,ymax),xaxt="n");
+axis(1,axTicks(1), format(axTicks(1), scientific=F))
 abline(v=m,lty=2)
 abline(v=m75,lty=2)
 abline(v=m25,lty=2)
@@ -58,5 +60,6 @@ dev.off()
 outfile = paste(outputDir, "binnedTiTv_hist.", annotationName, ".pdf", sep="")
 pdf(outfile, height=7, width=7)
 par(cex=1.1)
-plot(all$value,all$numVariants,xlab=annotationName,ylab="num Variants in bin",type="h");
+plot(all$value,all$numVariants,xlab=annotationName,ylab="num Variants in bin",type="h",xaxt="n");
+axis(1,axTicks(1), format(axTicks(1), scientific=F))
 dev.off()
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
index 7b647385d..f919667a9 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
@@ -56,6 +56,8 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
     private int MIN_VARIANTS_PER_BIN = 1000;
     @Argument(fullName = "max_variants_per_bin", shortName = "maxBinSize", doc = "The maximum number of variants in a bin.", required = false)
     private int MAX_VARIANTS_PER_BIN = 20000;
+    @Argument(fullName = "sampleName", shortName = "sampleName", doc = "Only process variants for this sample.", required = false)
+    private String SAMPLE_NAME = null;
 
 
     /////////////////////////////
@@ -95,7 +97,7 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
                 if( rod != null && rod instanceof RodVCF ) {
                     RodVCF variant = (RodVCF) rod;
                     if( variant.isSNP() ) {
-                        dataManager.addAnnotations( variant );
+                        dataManager.addAnnotations( variant, SAMPLE_NAME );
                     }
                 }
             }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
index 3b4ca52e9..cd3be3640 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
@@ -53,7 +53,13 @@ public class AnnotationDataManager {
         dataTruthSet = new HashMap<String, TreeSet<AnnotationDatum>>();
     }
 
-    public void addAnnotations( RodVCF variant ) {
+    public void addAnnotations( RodVCF variant, String sampleName ) {
+
+        if( sampleName != null ) { // only process variants that are found in the sample with this sampleName
+            if( variant.getGenotype(sampleName).isNoCall() ) { // this variant isn't found in this sample so break out
+                return;
+            }
+        } // else, process all samples
 
         // Loop over each annotation in the vcf record
         final Map<String,String> infoField = variant.getInfoValues();