diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
index 6bd92776e..4b3ad9ce1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
@@ -51,6 +51,9 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
     @Argument(fullName="minMAPQ", shortName = "minMAPQ", doc="If provided, we will also list read counts with MAPQ >= this value at a locus in coverage",required=false)
     protected int excludeMAPQBelowThis = -1;
 
+    @Argument(fullName="minDepth", shortName = "minDepth", doc="If provided, we will also list the percentage of loci with depth >= this value per interval",required=false)
+    protected int minDepthForPercentage = -1;
+
     @Argument(fullName="byReadGroup", shortName="byRG", doc="List read depths for each read group")
     protected boolean byReadGroup = false;
 
@@ -153,6 +156,9 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
         sum.totalCoverage += value.totalCoverage;
         sum.numDeletions += value.numDeletions;
         sum.numBadMQReads += value.numBadMQReads;
+        if ( value.totalCoverage >= minDepthForPercentage ) {
+            sum.minDepthCoveredLoci++;
+        }
         if ( byReadGroup ) {
             for ( String rg : readGroupNames ) {
                 int oldDepth = sum.depthByReadGroup.get(rg);
@@ -179,6 +185,10 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
             header.append("\taverage_coverage_atleast_MQ");
             header.append(excludeMAPQBelowThis);
         }
+        if ( minDepthForPercentage >= 0 ) {
+            header.append("\tpercent_loci_covered_atleast_depth");
+            header.append(minDepthForPercentage);            
+        }
         if ( byReadGroup ) {
             for ( String rg : readGroupNames ) {
                 header.append("\tcoverage_for_");
@@ -199,28 +209,34 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
 
     private void printDoCInfo(GenomeLoc loc, DoCInfo info, boolean printAverageCoverage) {
 
+        double totalBases = (double)(loc.getStop() - loc.getStart() + 1);
+
         StringBuilder sb = new StringBuilder();
         sb.append(loc);
         sb.append("\t");
         sb.append(info.totalCoverage);
         sb.append("\t");
         if ( printAverageCoverage ) {
-            sb.append(String.format("%.2f", ((double)info.totalCoverage) / (double)(loc.getStop() - loc.getStart() + 1)));
+            sb.append(String.format("%.2f", ((double)info.totalCoverage) / totalBases));
             sb.append("\t");
         }
         sb.append((info.totalCoverage - info.numDeletions));
         if ( printAverageCoverage ) {
             sb.append("\t");
-            sb.append(String.format("%.2f", ((double)(info.totalCoverage - info.numDeletions)) / (double)(loc.getStop() - loc.getStart() + 1)));
+            sb.append(String.format("%.2f", ((double)(info.totalCoverage - info.numDeletions)) / totalBases));
         }
         if ( excludeMAPQBelowThis > 0 ) {
             sb.append("\t");
             sb.append((info.totalCoverage - info.numBadMQReads));
             if ( printAverageCoverage ) {
                 sb.append("\t");
-                sb.append(String.format("%.2f", ((double)(info.totalCoverage - info.numBadMQReads)) / (double)(loc.getStop() - loc.getStart() + 1)));
+                sb.append(String.format("%.2f", ((double)(info.totalCoverage - info.numBadMQReads)) / totalBases));
             }
         }
+        if ( minDepthForPercentage >= 0 ) {
+            sb.append("\t");
+            sb.append(String.format("%.2f", ((double)info.minDepthCoveredLoci) / totalBases));            
+        }
         if ( byReadGroup ) {
             for ( String rg : readGroupNames ) {
                 sb.append("\t");
@@ -242,6 +258,7 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
         public int totalCoverage = 0;
         public int numDeletions = 0;
         public int numBadMQReads = 0;
+        public int minDepthCoveredLoci = 0;
 
         public HashMap<String, Integer> depthByReadGroup = null;
         public HashMap<String, Integer> depthBySample = null;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PercentOfBasesCoveredWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PercentOfBasesCoveredWalker.java
deleted file mode 100644
index f09e5bc31..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PercentOfBasesCoveredWalker.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
-
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.By;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.Pair;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-
-/**
- * Created by IntelliJ IDEA.
- * User: Ghost
- * Date: Nov 25, 2009
- * Time: 7:54:42 PM
- * To change this template use File | Settings | File Templates.
- */
-@By(DataSource.REFERENCE)
-public class PercentOfBasesCoveredWalker extends LocusWalker<Boolean, Pair<Integer,Integer>> implements TreeReducible<Pair<Integer,Integer>> {
-    @Argument(fullName="minimumDepth", shortName="minDepth", doc="Minimum depth beyond which to discount the base as uncovered", required=false)
-    int minDepth = 0;
-    @Argument(fullName="includeName",doc="include this name in the output of this walker (e.g. NAME: percent of bases covered . . .) ", required=false)
-    String name = null;
-    public void initialize() {
-        // do nothing
-    }
-
-    public Pair<Integer,Integer> reduceInit() {
-        return new Pair<Integer,Integer>(0,1); // robust initialization -- seen one base with zero coverage
-    }
-
-    public Boolean map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        return context.size() > minDepth;
-    }
-
-    public Pair<Integer,Integer> reduce(Boolean map, Pair<Integer,Integer> prevReduce) {
-        if ( map.booleanValue() ) {
-            return new Pair<Integer,Integer>(prevReduce.first+1,prevReduce.second+1);
-        } else {
-            return new Pair<Integer,Integer>(prevReduce.first,prevReduce.second+1);
-        }
-    }
-
-    public Pair<Integer,Integer> treeReduce( Pair<Integer,Integer> left, Pair<Integer,Integer> right) {
-        right.set(right.first+left.first,right.second+left.second);
-        return right;
-    }
-
-    public void onTraversalDone(Pair<Integer,Integer> reduceFinal) {
-        String msg;
-        if (name == null)
-            msg = "Percent of bases covered at "+minDepth+"x=";
-        else
-            msg = name+": Percent of bases covered at "+minDepth+"x=";
-        
-        out.printf("%s%s",msg,pair2percent(reduceFinal));
-    }
-
-    private String pair2percent(Pair<Integer,Integer> p ) {
-        return String.format("%d%s", (int) Math.floor( ( ( double) p.first*100.0) / p.second ), "%" );
-    }
-}
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
index ab47ed0b7..e56772722 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
@@ -15,6 +15,8 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
     static {
         expectations.put("-minMAPQ 1", "59c6071105a598e19f460640c35768c6");
         expectations.put("-minMAPQ 100", "e997fb5d61eaec21518722b0de90af20");
+        expectations.put("-minDepth 8", "3e50afef0e751119cd27c324bdfae544");
+        expectations.put("-minDepth 10", "d4c336d9e748347e1082bbc92d2489a3");
         expectations.put("-bySample", "160ffa185dbfa8b0d2dc57f60f5b1e48");
         expectations.put("-byRG", "dd3b4d040df7325dad4760ac6fa5252d");
         expectations.put("-minMAPQ 1 -bySample -byRG", "bd2a07ef548b86e82ac6cce534225612");