diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
index 014ed6dcb..54fc6e97e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
@@ -47,16 +47,15 @@
 package org.broadinstitute.sting.gatk.walkers.diagnostics.missing;
 
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Gather;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
-import org.broadinstitute.sting.gatk.walkers.By;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
+import org.broadinstitute.sting.gatk.report.GATKReportGatherer;
+import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
@@ -109,10 +108,12 @@ import java.util.List;
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
 @By(DataSource.REFERENCE)
+@PartitionBy(PartitionType.INTERVAL)
 public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics> implements NanoSchedulable {
     /**
      * A single GATKReport table with the qualifications on why the intervals passed by the -L argument were missing.
      */
+    @Gather(GATKReportGatherer.class)
     @Output
     protected PrintStream out;
 
@@ -125,11 +126,10 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     public String targetsFile;
 
     /**
-     * List of coding sequence intervals (exons) if different from the targets file, to distinguish intervals
-     * that overlap the cds and intervals that don't.
+     * List of baits to distinguish untargeted intervals from those that are targeted but not covered
      */
-    @Argument(shortName = "cds", required = false)
-    public String cdsFile = null;
+    @Argument(shortName = "baits", required = false)
+    public String baitsFile = null;
 
     /**
      * This value will be used to determine whether or not an interval had too high or too low GC content to be
@@ -182,8 +182,8 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
     }
 
     GATKReport simpleReport;
-    GenomeLocSortedSet target;
-    GenomeLocSortedSet cds;
+    GenomeLocSortedSet targets;
+    GenomeLocSortedSet baits;
 
     public boolean isReduceByInterval() {
         return true;
@@ -191,13 +191,13 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
 
     public void initialize() {
         // if cds file is not provided, just use the targets file (no harm done)
-        if (cdsFile == null)
-            cdsFile = targetsFile;
+        if (baitsFile == null)
+            baitsFile = targetsFile;
 
-        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "CD", "LN", "DS");
+        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "INTERVAL", "GC", "BQ", "MQ", "DP", "POS_IN_TARGET", "TARGET_SIZE", "BAITED", "MISSING_SIZE", "INTERPRETATION");
         final GenomeLocParser parser = getToolkit().getGenomeLocParser();
-        target = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
-        cds = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, cdsFile));
+        targets = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
+        baits = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, baitsFile));
     }
 
     public Metrics reduceInit() {
@@ -240,7 +240,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         for (Pair<GenomeLoc, Metrics> r : results) {
             final GenomeLoc interval = r.getFirst();
             final Metrics metrics = r.getSecond();
-            final List<GenomeLoc> overlappingIntervals = target.getOverlapping(interval);
+            final List<GenomeLoc> overlappingIntervals = targets.getOverlapping(interval);
 
             simpleReport.addRow(
                     interval.toString(),
@@ -250,7 +250,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
                     metrics.depth(),
                     getPositionInTarget(interval, overlappingIntervals),
                     getTargetSize(overlappingIntervals),
-                    cds.overlaps(interval),
+                    baits.overlaps(interval),
                     interval.size(),
                     interpret(metrics, interval)
             );
diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
index e9ccebf34..5e7c3ec86 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
@@ -42,23 +42,21 @@ public class GATKReportGatherer extends Gatherer {
         try {
             o = new PrintStream(output);
         } catch (FileNotFoundException e) {
-            throw new UserException("File to be output by CoverageByRG Gather function was not found");
+            throw new UserException(String.format("File %s to be output by GATKReportGatherer function was not found", output));
         }
 
         GATKReport current = new GATKReport();
         boolean isFirst = true;
         for (File input : inputs) {
-
-            // If the table is empty
             if (isFirst) {
                 current = new GATKReport(input);
                 isFirst = false;
             } else {
-                GATKReport toAdd = new GATKReport(input);
-                current.concat(toAdd);
+                current.concat(new GATKReport(input));
             }
         }
 
         current.print(o);
+        o.close();
     }
 }