diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
index 577781de9..cebec8c88 100755
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.utils.interval.IntervalUtils
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource
 import net.sf.samtools.SAMFileHeader
 import java.util.Collections
-import org.broadinstitute.sting.utils.GenomeLocParser
+import org.broadinstitute.sting.utils.{GenomeLoc, GenomeLocSortedSet, GenomeLocParser}
 
 case class GATKIntervals(reference: File, intervals: List[String]) {
   private lazy val referenceDataSource = new ReferenceDataSource(reference)
@@ -42,11 +42,15 @@ case class GATKIntervals(reference: File, intervals: List[String]) {
     header
   }
 
-  lazy val locs = {
+  lazy val locs: List[GenomeLoc] = {
     val parser = new GenomeLocParser(referenceDataSource.getReference)
-    val parsedLocs = IntervalUtils.parseIntervalArguments(parser, intervals, false)
+    val parsedLocs =
+      if (intervals.isEmpty)
+        GenomeLocSortedSet.createSetFromSequenceDictionary(samFileHeader.getSequenceDictionary).toList
+      else
+        IntervalUtils.parseIntervalArguments(parser, intervals, false)
     Collections.sort(parsedLocs)
-    parsedLocs
+    parsedLocs.toList
   }
 
   lazy val contigs = locs.map(_.getContig).distinct
diff --git a/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
new file mode 100644
index 000000000..663f6830a
--- /dev/null
+++ b/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
@@ -0,0 +1,63 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.queue.extensions.gatk
+
+import java.io.File
+import org.testng.Assert
+import org.testng.annotations.Test
+import org.broadinstitute.sting.BaseTest
+import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile
+import org.broadinstitute.sting.utils.{GenomeLocSortedSet, GenomeLocParser}
+import collection.JavaConversions._
+
+class GATKIntervalsUnitTest {
+  private final lazy val reference = new File(BaseTest.hg18Reference)
+  private final lazy val genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(reference))
+  private final lazy val referenceLocs = GenomeLocSortedSet.
+    createSetFromSequenceDictionary(new ReferenceDataSource(reference).getReference.getSequenceDictionary).toList.toList
+
+  @Test
+  def testWithIntervals() {
+    val chr1 = genomeLocParser.parseGenomeInterval("chr1:1-1")
+    val chr2 = genomeLocParser.parseGenomeInterval("chr2:2-3")
+    val chr3 = genomeLocParser.parseGenomeInterval("chr3:3-5")
+
+    val gi = new GATKIntervals(reference, List("chr1:1-1", "chr2:2-3", "chr3:3-5"))
+    Assert.assertEquals(gi.locs, List(chr1, chr2, chr3))
+    Assert.assertEquals(gi.contigs, List("chr1", "chr2", "chr3"))
+    Assert.assertEquals(gi.getSplits(2).toList, List(2, 3))
+    Assert.assertEquals(gi.getSplits(3).toList, List(1, 2, 3))
+  }
+
+  @Test
+  def testEmptyIntervals() {
+    val gi = new GATKIntervals(reference, Nil)
+    Assert.assertEquals(gi.locs, referenceLocs)
+    Assert.assertEquals(gi.contigs.size, referenceLocs.size)
+    Assert.assertEquals(gi.getSplits(2).toList, List(10, 45))
+    Assert.assertEquals(gi.getSplits(4).toList, List(5, 10, 16, 45))
+  }
+}