diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 4ea246108..7e5cb30a1 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -743,7 +743,7 @@ public class GenomeAnalysisEngine {
             else
                 throw new StingException("The GATK cannot currently process unindexed BAM files");
 
-            return new MonolithicShardStrategy(shardType);
+            return new MonolithicShardStrategy(shardType,drivingDataSource.getSequenceDictionary());
         }
 
         ShardStrategy shardStrategy = null;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
index 1214beeb2..e42a7a3c0 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
@@ -2,9 +2,14 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Collections;
 import java.util.List;
+import java.util.ArrayList;
+
+import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.SAMSequenceRecord;
 
 /**
  * A single, monolithic shard bridging all available data.
@@ -15,16 +20,24 @@ public class MonolithicShard implements Shard {
     /**
      * What type of MonolithicShard is this?  Read or locus?
      */
-    private ShardType shardType;
+    private final ShardType shardType;
+
+    /**
+     * Locations.  For the monolithic shard, should be a list of all available contigs in the reference.
+     */
+    private final List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
 
     /**
      * Creates a new monolithic shard of the given type.
      * @param shardType Type of the shard.  Must be either read or locus; cannot be intervalic.
+     * @param sequenceDictionary the sequence dictionary from which to derive contig info. 
      */
-    public MonolithicShard(ShardType shardType) {
+    public MonolithicShard(ShardType shardType, SAMSequenceDictionary sequenceDictionary) {
         if(shardType != ShardType.LOCUS && shardType != ShardType.READ)
             throw new StingException("Invalid shard type for monolithic shard: " + shardType);
         this.shardType = shardType;
+        for(SAMSequenceRecord sequenceRecord: sequenceDictionary.getSequences())
+            locs.add(GenomeLocParser.createGenomeLoc(sequenceRecord.getSequenceName(),1,sequenceRecord.getSequenceLength()));
     }
 
     /**
@@ -32,7 +45,7 @@ public class MonolithicShard implements Shard {
      * @return null.
      */
     public List<GenomeLoc> getGenomeLocs() {
-        return Collections.emptyList();
+        return locs;
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
index b90f3d147..022213d37 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
@@ -6,6 +6,8 @@ import org.broadinstitute.sting.utils.StingException;
 import java.util.Iterator;
 import java.util.NoSuchElementException;
 
+import net.sf.samtools.SAMSequenceDictionary;
+
 /**
  * Create a giant shard representing all the data in the input BAM(s).
  *
@@ -22,8 +24,8 @@ public class MonolithicShardStrategy implements ShardStrategy {
      * Create a new shard strategy for shards of the given type.
      * @param shardType The shard type.
      */
-    public MonolithicShardStrategy(Shard.ShardType shardType) {
-        shard = new MonolithicShard(shardType);
+    public MonolithicShardStrategy(final Shard.ShardType shardType, final SAMSequenceDictionary sequenceDictionary) {
+        shard = new MonolithicShard(shardType,sequenceDictionary);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
index 24964d51d..ce2b39fb4 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
@@ -122,8 +122,7 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
 
         public boolean hasNext() {
             // locus == null when doing monolithic sharding.
-            // TODO: Move the monolithic sharding iterator so that we don't have to special case here.
-            return sourceIterator.hasNext() && (locus == null || sourceIterator.peek().getLocation().overlapsP(locus));
+            return sourceIterator.hasNext() && sourceIterator.peek().getLocation().overlapsP(locus);
         }
 
         public AlignmentContext next() {
@@ -137,9 +136,6 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
 
         public void seedNextLocus() {
             // locus == null when doing monolithic sharding.
-            // TODO: Move the monolithic sharding iterator so that we don't have to special case here.
-            if(locus == null) return;
-
             while(sourceIterator.hasNext() && sourceIterator.peek().getLocation().isBefore(locus))
                 sourceIterator.next();                
         }