diff --git a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
index 1e4625bf0..3a6d88264 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
@@ -28,24 +28,25 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.util.Interval;
 import net.sf.picard.util.IntervalList;
 import net.sf.samtools.SAMFileHeader;
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.ArgumentException;
+import org.broadinstitute.sting.commandline.IntervalBinding;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.walkers.PrintReadsWalker;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.interval.IntervalSetRule;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.PrintWriter;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 
@@ -72,7 +73,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
 
         Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
-        samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"),  new Tags()));
+        samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
         samFiles.add(new SAMReaderID(new File("public/testdata/exampleNORG.bam"), new Tags()));
         samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"),  new Tags()));
         samFiles.add(new SAMReaderID(new File("public/testdata/exampleNORG.bam"), new Tags()));
@@ -108,16 +109,6 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         };
     }
 
-    @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
-    public void testInvalidRODIntervalHandling(GenomeAnalysisEngine testEngine, GenomeLocParser genomeLocParser,
-                                               String contig, int intervalStart, int intervalEnd ) throws Exception {
-
-        List<String> intervalArgs = new ArrayList<String>();
-        List<GenomeLoc> rodIntervals = Arrays.asList(genomeLocParser.createGenomeLoc(contig, intervalStart, intervalEnd, true));
-
-        testEngine.loadIntervals(intervalArgs, rodIntervals);
-    }
-
     @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
     public void testInvalidBedIntervalHandling(GenomeAnalysisEngine testEngine, GenomeLocParser genomeLocParser,
                                                String contig, int intervalStart, int intervalEnd ) throws Exception {
@@ -126,10 +117,10 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         File bedFile = createTempFile("testInvalidBedIntervalHandling", ".bed",
                                       String.format("%s %d %d", contig, intervalStart -1, intervalEnd));
 
-        List<String> intervalArgs = Arrays.asList(bedFile.getAbsolutePath());
-        List<GenomeLoc> rodIntervals = new ArrayList<GenomeLoc>();
+        List<IntervalBinding<Feature>> intervalArgs = new ArrayList<IntervalBinding<Feature>>(1);
+        intervalArgs.add(new IntervalBinding<Feature>(bedFile.getAbsolutePath()));
 
-        testEngine.loadIntervals(intervalArgs, rodIntervals);
+        testEngine.loadIntervals(intervalArgs, IntervalSetRule.UNION);
     }
 
     @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
@@ -144,10 +135,10 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         File picardIntervalFile = createTempFile("testInvalidPicardIntervalHandling", ".intervals");
         picardIntervals.write(picardIntervalFile);
 
-        List<String> intervalArgs = Arrays.asList(picardIntervalFile.getAbsolutePath());
-        List<GenomeLoc> rodIntervals = new ArrayList<GenomeLoc>();
+        List<IntervalBinding<Feature>> intervalArgs = new ArrayList<IntervalBinding<Feature>>(1);
+        intervalArgs.add(new IntervalBinding<Feature>(picardIntervalFile.getAbsolutePath()));
 
-        testEngine.loadIntervals(intervalArgs, rodIntervals);
+        testEngine.loadIntervals(intervalArgs, IntervalSetRule.UNION);
     }
 
     @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
@@ -157,10 +148,10 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         File gatkIntervalFile = createTempFile("testInvalidGATKFileIntervalHandling", ".intervals",
                                                String.format("%s:%d-%d", contig, intervalStart, intervalEnd));
 
-        List<String> intervalArgs = Arrays.asList(gatkIntervalFile.getAbsolutePath());
-        List<GenomeLoc> rodIntervals = new ArrayList<GenomeLoc>();
+        List<IntervalBinding<Feature>> intervalArgs = new ArrayList<IntervalBinding<Feature>>(1);
+        intervalArgs.add(new IntervalBinding<Feature>(gatkIntervalFile.getAbsolutePath()));
 
-        testEngine.loadIntervals(intervalArgs, rodIntervals);
+        testEngine.loadIntervals(intervalArgs, IntervalSetRule.UNION);
     }
 
     private File createTempFile( String tempFilePrefix, String tempFileExtension, String... lines ) throws Exception {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
index 3a242cb13..f37890ee3 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.gatk.arguments;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.commandline.IntervalBinding;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -84,9 +86,9 @@ public class GATKArgumentCollectionUnitTest extends BaseTest {
         collect.unsafe = ValidationExclusion.TYPE.ALL;
         collect.downsampleFraction = null;
         collect.downsampleCoverage = null;
-        collect.intervals = new ArrayList<String>();
-        collect.intervals.add("intervals".toLowerCase());
-        collect.excludeIntervals = new ArrayList<String>();
+        collect.intervals = new ArrayList<IntervalBinding<Feature>>();
+        collect.intervals.add(new IntervalBinding<Feature>("intervals".toLowerCase()));
+        collect.excludeIntervals = new ArrayList<IntervalBinding<Feature>>();
         collect.numberOfThreads = 1;
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
index 379d79c84..1431a80f3 100644
--- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
@@ -48,19 +48,20 @@ public class IntervalIntegrationTest extends WalkerTest {
         executeTest("testAllIntervalsImplicit",spec);
     }
 
-    @Test(enabled = true)
-    public void testAllExplicitIntervalParsing() {
-        String md5 = "7821db9e14d4f8e07029ff1959cd5a99";
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T CountLoci" +
-                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
-                        " -R " + hg18Reference +
-                        " -L all" +
-                        " -o %s",
-                        1, // just one output file
-                        Arrays.asList(md5));                        
-        executeTest("testAllIntervalsExplicit",spec);
-    }
+// '-L all' is no longer supported
+//    @Test(enabled = true)
+//    public void testAllExplicitIntervalParsing() {
+//        String md5 = "7821db9e14d4f8e07029ff1959cd5a99";
+//        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+//                "-T CountLoci" +
+//                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+//                        " -R " + hg18Reference +
+//                        " -L all" +
+//                        " -o %s",
+//                        1, // just one output file
+//                        Arrays.asList(md5));
+//        executeTest("testAllIntervalsExplicit",spec);
+//    }
 
     @Test
     public void testUnmappedReadInclusion() {
@@ -102,5 +103,62 @@ public class IntervalIntegrationTest extends WalkerTest {
         executeTest("testUnmappedReadExclusion",spec);
     }
 
+    @Test(enabled = true)
+    public void testIntervalParsingFromFile() {
+        String md5 = "48a24b70a0b376535542b996af517398";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.1.vcf",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testIntervalParsingFromFile", spec);
+    }
 
+    @Test(enabled = true)
+    public void testIntervalMergingFromFiles() {
+        String md5 = "9ae0ea9e3c9c6e1b9b6252c8395efdc1";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.1.vcf" +
+                        " -L " + validationDataLocation + "intervalTest.2.vcf",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testIntervalMergingFromFiles", spec);
+    }
+
+    @Test(enabled = true)
+    public void testIntervalExclusionsFromFiles() {
+        String md5 = "26ab0db90d72e28ad0ba1e22ee510510";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.1.vcf" +
+                        " -XL " + validationDataLocation + "intervalTest.2.vcf",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testIntervalExclusionsFromFiles", spec);
+    }
+
+    @Test(enabled = true)
+    public void testMixedIntervalMerging() {
+        String md5 = "7c5aba41f53293b712fd86d08ed5b36e";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.1.vcf" +
+                        " -L chr1:1677524-1677528",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testMixedIntervalMerging", spec);
+    }
 }
diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
index 98b878d23..8794e03c6 100644
--- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java
@@ -69,7 +69,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
             hg19GenomeLocParser = new GenomeLocParser(seq);
             hg19ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()).toList()) ;
 
-            hg19exomeIntervals = Collections.unmodifiableList(IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(hg19Intervals), false));
+            hg19exomeIntervals = Collections.unmodifiableList(IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(hg19Intervals)));
         }
         catch(FileNotFoundException ex) {
             throw new UserException.CouldNotReadInputFile(hg19Ref,ex);
@@ -235,9 +235,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
         List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
         IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 1);
@@ -261,9 +261,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
         List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
         IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 1);
@@ -303,9 +303,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
         List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
         IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 1);
@@ -331,9 +331,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
         List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
         IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 1);
@@ -359,9 +359,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
         List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
         IntervalUtils.scatterFixedIntervals(hg18Header, splits, files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 2);
         Assert.assertEquals(locs2.size(), 1);
@@ -376,7 +376,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
     @Test
     public void testScatterFixedIntervalsFile() {
         List<File> files = testFiles("sg.", 20, ".intervals");
-        List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(BaseTest.GATKDataLocation + "whole_exome_agilent_designed_120.targets.hg18.chr20.interval_list"), false);
+        List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(BaseTest.GATKDataLocation + "whole_exome_agilent_designed_120.targets.hg18.chr20.interval_list"));
         List<List<GenomeLoc>> splits = IntervalUtils.splitFixedIntervals(locs, files.size());
 
         int[] counts = {
@@ -401,7 +401,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
         int locIndex = 0;
         for (int i = 0; i < files.size(); i++) {
             String file = files.get(i).toString();
-            List<GenomeLoc> parsedLocs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(file), false);
+            List<GenomeLoc> parsedLocs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(file));
             Assert.assertEquals(parsedLocs.size(), counts[i], "Intervals in " + file);
             for (GenomeLoc parsedLoc: parsedLocs)
                 Assert.assertEquals(parsedLoc, locs.get(locIndex), String.format("Genome loc %d from file %d", locIndex++, i));
@@ -417,7 +417,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
         for (int i = 0; i < files.size(); i++) {
             String file = files.get(i).toString();
-            List<GenomeLoc> parsedLocs = IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(file), false);
+            List<GenomeLoc> parsedLocs = IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(file));
             Assert.assertEquals(parsedLocs.size(), 1, "parsedLocs[" + i + "].size()");
             Assert.assertEquals(parsedLocs.get(0), hg19ReferenceLocs.get(i), "parsedLocs[" + i + "].get()");
         }
@@ -434,9 +434,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
         IntervalUtils.scatterContigIntervals(hg18Header, getLocs(intervals), files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 1);
@@ -457,9 +457,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
         IntervalUtils.scatterContigIntervals(hg18Header, getLocs("chr1", "chr2", "chr3"), files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 1);
@@ -481,9 +481,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
         IntervalUtils.scatterContigIntervals(hg18Header, getLocs("chr1", "chr2", "chr3", "chr4"), files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 1);
@@ -513,9 +513,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
         IntervalUtils.scatterContigIntervals(hg18Header, getLocs(intervals), files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 2);
         Assert.assertEquals(locs2.size(), 1);
@@ -539,9 +539,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
         IntervalUtils.scatterContigIntervals(hg18Header, getLocs(intervals), files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 2);
@@ -565,9 +565,9 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
         IntervalUtils.scatterContigIntervals(hg18Header, getLocs(intervals), files);
 
-        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()), false);
-        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()), false);
-        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()), false);
+        List<GenomeLoc> locs1 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(0).toString()));
+        List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
+        List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
 
         Assert.assertEquals(locs1.size(), 1);
         Assert.assertEquals(locs2.size(), 1);
@@ -586,7 +586,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
         for (int i = 0; i < files.size(); i++) {
             String file = files.get(i).toString();
-            List<GenomeLoc> parsedLocs = IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(file), false);
+            List<GenomeLoc> parsedLocs = IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, Arrays.asList(file));
             Assert.assertEquals(parsedLocs.size(), 1, "parsedLocs[" + i + "].size()");
             Assert.assertEquals(parsedLocs.get(0), hg19ReferenceLocs.get(i), "parsedLocs[" + i + "].get()");
         }
@@ -610,7 +610,7 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
     @Test(dataProvider="unmergedIntervals")
     public void testUnmergedIntervals(String unmergedIntervals) {
-        List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Collections.singletonList(validationDataLocation + unmergedIntervals), false);
+        List<GenomeLoc> locs = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Collections.singletonList(validationDataLocation + unmergedIntervals));
         Assert.assertEquals(locs.size(), 2);
 
         List<GenomeLoc> merged = IntervalUtils.mergeIntervalLocations(locs, IntervalMergingRule.ALL);
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
index 0fb997f43..9e47f64a1 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
@@ -48,7 +48,7 @@ case class GATKIntervals(reference: File, intervals: List[String]) {
       if (intervals.isEmpty)
         GenomeLocSortedSet.createSetFromSequenceDictionary(samFileHeader.getSequenceDictionary).toList
       else
-        IntervalUtils.parseIntervalArguments(parser, intervals, false)
+        IntervalUtils.parseIntervalArguments(parser, intervals)
     Collections.sort(parsedLocs)
     Collections.unmodifiableList(parsedLocs)
   }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
index 32e58ca6a..98392e493 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
@@ -69,8 +69,6 @@ trait GATKScatterFunction extends ScatterFunction {
   }
 
   override def isScatterGatherable = {
-    if (this.originalGATK.BTI != null && this.originalGATK.BTIMR == null)
-      throw new IllegalArgumentException("BTI requires BTIMR for use with scatter-gather (recommended: INTERSECTION)")
     this.originalGATK.reference_sequence != null
   }