diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantSummary.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantSummary.java
index 342de4dde5c..32b6d951f88 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantSummary.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantSummary.java
@@ -167,9 +167,10 @@ private boolean overlapsKnownCNV(VariantContext cnv, VariantEvalContext context)
         if ( knownCNVs != null ) {
             List<Feature> overlaps = context.queryFeaturesIncludingOverlapping(knownCNVs, new SimpleInterval(cnv.getContig(), cnv.getStart(), cnv.getEnd()));
             GenomeLocParser parser = new GenomeLocParser(context.getSequenceDictionaryForDrivingVariants());
-            GenomeLoc loc1 = parser.createGenomeLoc(cnv);
+            // NOTE: by using this overload we are explicitly allowing variants that don't correctly overlap the reference intervals
+            GenomeLoc loc1 = parser.createGenomeLoc(cnv, false);
             for (Feature vc : overlaps) {
-                GenomeLoc loc2 = parser.createGenomeLoc(vc);
+                GenomeLoc loc2 = parser.createGenomeLoc(vc, false);
                 final double overlapP = loc1.reciprocialOverlapFraction(loc2);
                 if ( overlapP > MIN_CNV_OVERLAP )
                     return true;
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java b/src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java
index 42a886fe020..c5c8041ac3f 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java
@@ -393,7 +393,15 @@ public GenomeLoc createGenomeLoc( final GATKRead read ) {
      * @return
      */
     public GenomeLoc createGenomeLoc(final Feature feature) {
-        return createGenomeLoc(feature.getContig(), feature.getStart(), feature.getEnd());
+        return createGenomeLoc(feature.getContig(), feature.getStart(), feature.getEnd(), true);
+    }
+
+    /**
+     * Creates a GenomeLoc from a Tribble feature
+     * @return
+     */
+    public GenomeLoc createGenomeLoc(final Feature feature, final boolean mustBeOnReference) {
+        return createGenomeLoc(feature.getContig(), feature.getStart(), feature.getEnd(), mustBeOnReference);
     }
 
     /**
@@ -405,7 +413,7 @@ public GenomeLoc createGenomeLoc(final Feature feature) {
      */
     public GenomeLoc createGenomeLoc(final Locatable locatable) {
         Utils.nonNull(locatable, "the input locatable cannot be null");
-        return createGenomeLoc(locatable.getContig(), locatable.getStart(), locatable.getEnd());
+        return createGenomeLoc(locatable.getContig(), locatable.getStart(), locatable.getEnd(), false);
     }
 
     /**
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java
index a9cf8d861f1..8ec3893116b 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java
@@ -357,7 +357,7 @@ public static List<GenomeLoc> featureFileToIntervals( final GenomeLocParser pars
             final List<GenomeLoc> featureIntervals = new ArrayList<>();
 
             for ( final Feature feature : dataSource ) {
-                featureIntervals.add(parser.createGenomeLoc(feature));
+                featureIntervals.add(parser.createGenomeLoc(feature, true));
             }
             return featureIntervals;
         }
diff --git a/src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java
index 8471f2ef9bf..6da70ba0fad 100644
--- a/src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java
@@ -608,6 +608,29 @@ public void testUseAllHG38ContigsInIntervalQuery() {
         );
     }
 
+    @Test(expectedExceptions = UserException.MalformedGenomeLoc.class)
+    public void testReasonableErrorWithInvalidBedFile() throws IOException {
+        File outOfBoundsBedFile = new File(INTERVAL_TEST_DATA + "bad_hg19_interval_span.bed"); // this bed file has a bogus interval the extends past the end chr1 and should throw an exception
+        // this should throw a user exception because of the invalid interval
+        IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, outOfBoundsBedFile.getAbsolutePath());
+    }
+
+    @Test(expectedExceptions = UserException.MalformedGenomeLoc.class)
+    public void testReasonableErrorWithInvalidListFile() throws IOException {
+        File outOfBoundListFile = new File(INTERVAL_TEST_DATA + "bad_hg19_example_intervals.list"); // this list file has a bogus interval the extends past the end chr1 and should throw an exception
+        // this should throw a user exception because of the invalid interval
+        IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, outOfBoundListFile.getAbsolutePath());
+    }
+
+    //NOTE the .interval_list style argument input gets handled differently from the other -L inputs but we still get a reasonable exception in this case
+    @Test(expectedExceptions = UserException.MalformedFile.class)
+    public void testReasonableErrorWithInvalidPicardListFile() throws IOException {
+        File outOfBoundsIntervalListFile = new File(INTERVAL_TEST_DATA + "bad_hg19.interval_list"); // this list file has a bogus interval the extends past the end chr1 and should throw an exception
+        // this should throw a user exception because of the invalid interval
+        IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, outOfBoundsIntervalListFile.getAbsolutePath());
+    }
+
+
     @Test
     public void testResolveAmbiguousIntervalQueryUsingBEDFormat() throws IOException {
         // For the rare case where an interval query is ambiguous, make sure it can be resolved by using a bed file.
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19.interval_list b/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19.interval_list
new file mode 100644
index 00000000000..40828fe2d29
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19.interval_list
@@ -0,0 +1,88 @@
+@HD	VN:1.6
+@SQ	SN:1	LN:249250621	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:1b22b98cdeb4a9304cb5d48026a85128	SP:Homo sapiens
+@SQ	SN:2	LN:243199373	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:a0d9851da00400dec1098a9255ac712e	SP:Homo sapiens
+@SQ	SN:3	LN:198022430	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:fdfd811849cc2fadebc929bb925902e5	SP:Homo sapiens
+@SQ	SN:4	LN:191154276	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:23dccd106897542ad87d2765d28a19a1	SP:Homo sapiens
+@SQ	SN:5	LN:180915260	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:0740173db9ffd264d728f32784845cd7	SP:Homo sapiens
+@SQ	SN:6	LN:171115067	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:1d3a93a248d92a729ee764823acbbc6b	SP:Homo sapiens
+@SQ	SN:7	LN:159138663	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:618366e953d6aaad97dbe4777c29375e	SP:Homo sapiens
+@SQ	SN:8	LN:146364022	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:96f514a9929e410c6651697bded59aec	SP:Homo sapiens
+@SQ	SN:9	LN:141213431	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:3e273117f15e0a400f01055d9f393768	SP:Homo sapiens
+@SQ	SN:10	LN:135534747	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:988c28e000e84c26d552359af1ea2e1d	SP:Homo sapiens
+@SQ	SN:11	LN:135006516	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:98c59049a2df285c76ffb1c6db8f8b96	SP:Homo sapiens
+@SQ	SN:12	LN:133851895	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:51851ac0e1a115847ad36449b0015864	SP:Homo sapiens
+@SQ	SN:13	LN:115169878	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:283f8d7892baa81b510a015719ca7b0b	SP:Homo sapiens
+@SQ	SN:14	LN:107349540	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:98f3cae32b2a2e9524bc19813927542e	SP:Homo sapiens
+@SQ	SN:15	LN:102531392	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:e5645a794a8238215b2cd77acb95a078	SP:Homo sapiens
+@SQ	SN:16	LN:90354753	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:fc9b1a7b42b97a864f56b348b06095e6	SP:Homo sapiens
+@SQ	SN:17	LN:81195210	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:351f64d4f4f9ddd45b35336ad97aa6de	SP:Homo sapiens
+@SQ	SN:18	LN:78077248	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c	SP:Homo sapiens
+@SQ	SN:19	LN:59128983	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:1aacd71f30db8e561810913e0b72636d	SP:Homo sapiens
+@SQ	SN:20	LN:63025520	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:0dec9660ec1efaaf33281c0d5ea2560f	SP:Homo sapiens
+@SQ	SN:21	LN:48129895	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:2979a6085bfe28e3ad6f552f361ed74d	SP:Homo sapiens
+@SQ	SN:22	LN:51304566	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:a718acaa6135fdca8357d5bfe94211dd	SP:Homo sapiens
+@SQ	SN:X	LN:155270560	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:7e0e2e580297b7764e31dbc80c2540dd	SP:Homo sapiens
+@SQ	SN:Y	LN:59373566	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:1fa3474750af0948bdf97d5a0ee52e51	SP:Homo sapiens
+@SQ	SN:MT	LN:16569	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:c68f52674c9fb33aef52dcf399755519	SP:Homo sapiens
+@SQ	SN:GL000207.1	LN:4262	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:f3814841f1939d3ca19072d9e89f3fd7	SP:Homo sapiens
+@SQ	SN:GL000226.1	LN:15008	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:1c1b2cd1fccbc0a99b6a447fa24d1504	SP:Homo sapiens
+@SQ	SN:GL000229.1	LN:19913	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:d0f40ec87de311d8e715b52e4c7062e1	SP:Homo sapiens
+@SQ	SN:GL000231.1	LN:27386	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:ba8882ce3a1efa2080e5d29b956568a4	SP:Homo sapiens
+@SQ	SN:GL000210.1	LN:27682	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:851106a74238044126131ce2a8e5847c	SP:Homo sapiens
+@SQ	SN:GL000239.1	LN:33824	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:99795f15702caec4fa1c4e15f8a29c07	SP:Homo sapiens
+@SQ	SN:GL000235.1	LN:34474	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:118a25ca210cfbcdfb6c2ebb249f9680	SP:Homo sapiens
+@SQ	SN:GL000201.1	LN:36148	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:dfb7e7ec60ffdcb85cb359ea28454ee9	SP:Homo sapiens
+@SQ	SN:GL000247.1	LN:36422	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:7de00226bb7df1c57276ca6baabafd15	SP:Homo sapiens
+@SQ	SN:GL000245.1	LN:36651	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:89bc61960f37d94abf0df2d481ada0ec	SP:Homo sapiens
+@SQ	SN:GL000197.1	LN:37175	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:6f5efdd36643a9b8c8ccad6f2f1edc7b	SP:Homo sapiens
+@SQ	SN:GL000203.1	LN:37498	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:96358c325fe0e70bee73436e8bb14dbd	SP:Homo sapiens
+@SQ	SN:GL000246.1	LN:38154	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:e4afcd31912af9d9c2546acf1cb23af2	SP:Homo sapiens
+@SQ	SN:GL000249.1	LN:38502	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:1d78abec37c15fe29a275eb08d5af236	SP:Homo sapiens
+@SQ	SN:GL000196.1	LN:38914	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:d92206d1bb4c3b4019c43c0875c06dc0	SP:Homo sapiens
+@SQ	SN:GL000248.1	LN:39786	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:5a8e43bec9be36c7b49c84d585107776	SP:Homo sapiens
+@SQ	SN:GL000244.1	LN:39929	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:0996b4475f353ca98bacb756ac479140	SP:Homo sapiens
+@SQ	SN:GL000238.1	LN:39939	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:131b1efc3270cc838686b54e7c34b17b	SP:Homo sapiens
+@SQ	SN:GL000202.1	LN:40103	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:06cbf126247d89664a4faebad130fe9c	SP:Homo sapiens
+@SQ	SN:GL000234.1	LN:40531	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:93f998536b61a56fd0ff47322a911d4b	SP:Homo sapiens
+@SQ	SN:GL000232.1	LN:40652	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:3e06b6741061ad93a8587531307057d8	SP:Homo sapiens
+@SQ	SN:GL000206.1	LN:41001	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:43f69e423533e948bfae5ce1d45bd3f1	SP:Homo sapiens
+@SQ	SN:GL000240.1	LN:41933	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:445a86173da9f237d7bcf41c6cb8cc62	SP:Homo sapiens
+@SQ	SN:GL000236.1	LN:41934	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:fdcd739913efa1fdc64b6c0cd7016779	SP:Homo sapiens
+@SQ	SN:GL000241.1	LN:42152	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:ef4258cdc5a45c206cea8fc3e1d858cf	SP:Homo sapiens
+@SQ	SN:GL000243.1	LN:43341	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:cc34279a7e353136741c9fce79bc4396	SP:Homo sapiens
+@SQ	SN:GL000242.1	LN:43523	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:2f8694fc47576bc81b5fe9e7de0ba49e	SP:Homo sapiens
+@SQ	SN:GL000230.1	LN:43691	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:b4eb71ee878d3706246b7c1dbef69299	SP:Homo sapiens
+@SQ	SN:GL000237.1	LN:45867	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:e0c82e7751df73f4f6d0ed30cdc853c0	SP:Homo sapiens
+@SQ	SN:GL000233.1	LN:45941	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:7fed60298a8d62ff808b74b6ce820001	SP:Homo sapiens
+@SQ	SN:GL000204.1	LN:81310	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:efc49c871536fa8d79cb0a06fa739722	SP:Homo sapiens
+@SQ	SN:GL000198.1	LN:90085	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:868e7784040da90d900d2d1b667a1383	SP:Homo sapiens
+@SQ	SN:GL000208.1	LN:92689	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:aa81be49bf3fe63a79bdc6a6f279abf6	SP:Homo sapiens
+@SQ	SN:GL000191.1	LN:106433	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:d75b436f50a8214ee9c2a51d30b2c2cc	SP:Homo sapiens
+@SQ	SN:GL000227.1	LN:128374	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:a4aead23f8053f2655e468bcc6ecdceb	SP:Homo sapiens
+@SQ	SN:GL000228.1	LN:129120	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:c5a17c97e2c1a0b6a9cc5a6b064b714f	SP:Homo sapiens
+@SQ	SN:GL000214.1	LN:137718	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:46c2032c37f2ed899eb41c0473319a69	SP:Homo sapiens
+@SQ	SN:GL000221.1	LN:155397	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:3238fb74ea87ae857f9c7508d315babb	SP:Homo sapiens
+@SQ	SN:GL000209.1	LN:159169	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:f40598e2a5a6b26e84a3775e0d1e2c81	SP:Homo sapiens
+@SQ	SN:GL000218.1	LN:161147	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:1d708b54644c26c7e01c2dad5426d38c	SP:Homo sapiens
+@SQ	SN:GL000220.1	LN:161802	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:fc35de963c57bf7648429e6454f1c9db	SP:Homo sapiens
+@SQ	SN:GL000213.1	LN:164239	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:9d424fdcc98866650b58f004080a992a	SP:Homo sapiens
+@SQ	SN:GL000211.1	LN:166566	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:7daaa45c66b288847b9b32b964e623d3	SP:Homo sapiens
+@SQ	SN:GL000199.1	LN:169874	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:569af3b73522fab4b40995ae4944e78e	SP:Homo sapiens
+@SQ	SN:GL000217.1	LN:172149	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:6d243e18dea1945fb7f2517615b8f52e	SP:Homo sapiens
+@SQ	SN:GL000216.1	LN:172294	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:642a232d91c486ac339263820aef7fe0	SP:Homo sapiens
+@SQ	SN:GL000215.1	LN:172545	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:5eb3b418480ae67a997957c909375a73	SP:Homo sapiens
+@SQ	SN:GL000205.1	LN:174588	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:d22441398d99caf673e9afb9a1908ec5	SP:Homo sapiens
+@SQ	SN:GL000219.1	LN:179198	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:f977edd13bac459cb2ed4a5457dba1b3	SP:Homo sapiens
+@SQ	SN:GL000224.1	LN:179693	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:d5b2fc04f6b41b212a4198a07f450e20	SP:Homo sapiens
+@SQ	SN:GL000223.1	LN:180455	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:399dfa03bf32022ab52a846f7ca35b30	SP:Homo sapiens
+@SQ	SN:GL000195.1	LN:182896	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:5d9ec007868d517e73543b005ba48535	SP:Homo sapiens
+@SQ	SN:GL000212.1	LN:186858	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:563531689f3dbd691331fd6c5730a88b	SP:Homo sapiens
+@SQ	SN:GL000222.1	LN:186861	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:6fe9abac455169f50470f5a6b01d0f59	SP:Homo sapiens
+@SQ	SN:GL000200.1	LN:187035	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:75e4c8d17cd4addf3917d1703cacaf25	SP:Homo sapiens
+@SQ	SN:GL000193.1	LN:189789	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:dbb6e8ece0b5de29da56601613007c2a	SP:Homo sapiens
+@SQ	SN:GL000194.1	LN:191469	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:6ac8f815bf8e845bb3031b73f812c012	SP:Homo sapiens
+@SQ	SN:GL000225.1	LN:211173	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:63945c3e6962f28ffd469719a747e73c	SP:Homo sapiens
+@SQ	SN:GL000192.1	LN:547496	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:325ba9e808f669dfeee210fdd7b470ac	SP:Homo sapiens
+@SQ	SN:NC_007605	LN:171823	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:6743bd63b3ff2b5b8985d8933c53290a	SP:Homo sapiens
+@SQ	SN:hs37d5	LN:35477943	UR:/seq/references/Homo_sapiens_assembly19_1000genomes_decoy/v1/Homo_sapiens_assembly19_1000genomes_decoy.fasta	AS:19	M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1	SP:Homo sapiens
+1	249240000	249260000	+	.
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19_example_intervals.list b/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19_example_intervals.list
new file mode 100644
index 00000000000..7d9525bbaf0
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19_example_intervals.list
@@ -0,0 +1,2 @@
+1:100-200
+1:249240000-249260000
diff --git a/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19_interval_span.bed b/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19_interval_span.bed
new file mode 100644
index 00000000000..2c496cf84b9
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/utils/interval/bad_hg19_interval_span.bed
@@ -0,0 +1 @@
+1	249240000	249260000