diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
index 46981f5e3..da21fc53c 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
@@ -35,6 +35,8 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
     @Argument(fullName="showSecondBaseQuals",doc="If true, prints out second base qualities in the pileup",required=false)
     public boolean showSecondBaseQuals = false;
 
+    @Argument(fullName="qualsAsInts",doc="If true, prints out qualities in the pileup as comma-separated integers",required=false)
+    public boolean qualsAsInts = false;
 
     @Argument(fullName="extended",shortName="ext",doc="extended",required=false)
     public boolean EXTENDED = false;
@@ -84,7 +86,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
             rodString = "[ROD: " + rodString + "]";
 
         //if ( context.getLocation().getStart() % 1 == 0 ) {
-        out.printf("%s%s %s%n", pileup.getPileupString(), extras, rodString);
+        out.printf("%s%s %s%n", pileup.getPileupString(qualsAsInts), extras, rodString);
         //}
 
         if ( EXTENDED ) {
diff --git a/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
index 047a9244c..cbefbf2c3 100755
--- a/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
@@ -78,7 +78,7 @@ public class ReadBackedPileup extends BasicPileup {
         return probDistPileupAsString(reads, offsets);
     }
 
-    public String getPileupString()
+    public String getPileupString(boolean qualsAsInts)
     {
         // In the pileup format, each line represents a genomic position, consisting of chromosome name,
         // coordinate, reference base, read bases, read qualities and alignment mapping qualities.
@@ -88,7 +88,7 @@ public class ReadBackedPileup extends BasicPileup {
                 getLocation().getContig(), getLocation().getStart(),    // chromosome name and coordinate
                 getRef(),                                               // reference base
                 getBases(),
-                getQuals(),
-                getMappingQuals());
+                qualsAsInts ? getQuals() : getQualsAsInts(),
+                qualsAsInts ? getMappingQuals() : getMappingQualsAsInts());
     }
 }
\ No newline at end of file