diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java
index 1536ef7d113..641804ca641 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java
@@ -412,14 +412,17 @@ public Object onTraversalSuccess() {
             return null;
         }
 
-        SimpleInterval interval = prevPos != null ? new SimpleInterval(prevPos.getContig(), prevPos.getStart(), variantContextsOverlappingCurrentMerge.stream().map(VariantContext::getEnd).max(Comparator.naturalOrder()).get()) :
-                storedReferenceContext.getInterval();
-
-        createIntermediateVariants(interval);
-
-        // there shouldn't be any state left unless the user cut in the middle of a gVCF block
         if ( !variantContextsOverlappingCurrentMerge.isEmpty() ) {
-            logger.warn("You have asked for an interval that cuts in the middle of one or more gVCF blocks. Please note that this will cause you to lose records that don't end within your interval.");
+            // finish off the last blocks
+            final SimpleInterval lastInterval = new SimpleInterval(
+                    variantContextsOverlappingCurrentMerge.get(0).getContig(),
+                    variantContextsOverlappingCurrentMerge.get(0).getStart(),
+                    variantContextsOverlappingCurrentMerge.stream().map(VariantContext::getEnd).max(Comparator.naturalOrder()).get());
+                createIntermediateVariants(lastInterval);
+            // there shouldn't be any state left unless the user cut in the middle of a gVCF block
+            if ( !variantContextsOverlappingCurrentMerge.isEmpty() ) {
+                logger.warn("You have asked for an interval that cuts in the middle of one or more gVCF blocks. Please note that this will cause you to lose records that don't end within your interval.");
+            }
         }
 
         return null;
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java
index 658feaae272..f7a80540a79 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java
@@ -74,7 +74,10 @@ public Object[][] gvcfsToCombine() {
                 //Testing allele-specific annotations
                 {new File[]{getTestFile("NA12878.AS.chr20snippet.g.vcf"), getTestFile("NA12892.AS.chr20snippet.g.vcf")}, getTestFile("testAlleleSpecificAnnotations.vcf"), Arrays.asList("-G", "Standard", "-G", "AS_Standard"), b37_reference_20_21},
                 //Testing allele-specific annotations missing AS_Standard Group
-                {new File[]{getTestFile("NA12878.AS.chr20snippet.g.vcf"), getTestFile("NA12892.AS.chr20snippet.g.vcf")}, getTestFile("testAlleleSpecificAnnotationsNoGroup.vcf"), Arrays.asList("-G", "Standard", "-G", "AS_Standard"), b37_reference_20_21},};
+                {new File[]{getTestFile("NA12878.AS.chr20snippet.g.vcf"), getTestFile("NA12892.AS.chr20snippet.g.vcf")}, getTestFile("testAlleleSpecificAnnotationsNoGroup.vcf"), Arrays.asList("-G", "Standard", "-G", "AS_Standard"), b37_reference_20_21},
+                //Test that trailing reference blocks are emitted with correct intervals
+                {new File[]{getTestFile("gvcfExample1WithTrailingReferenceBlocks.g.vcf"), getTestFile("gvcfExample2WithTrailingReferenceBlocks.g.vcf")}, getTestFile("gvcfWithTrailingReferenceBlocksExpected.g.vcf"), NO_EXTRA_ARGS, b38_reference_20_21},
+        };
     }
 
 
@@ -118,11 +121,6 @@ public void compareToGATK3(File[] inputs, File outputFile, List<String> extraArg
         } else {
             System.out.println("Found precomputed gatk3Result");
         }
-        final Path expectedResultsDir = Paths.get(getToolTestDataDir());
-        if ( !Files.exists(expectedResultsDir)) {
-            Files.createDirectory(expectedResultsDir);
-        }
-        Files.copy(gatk3Result.toPath(), expectedResultsDir.resolve(outputFile.getName()), StandardCopyOption.REPLACE_EXISTING);
 
         assertVariantContextsMatch(Arrays.asList(inputs), gatk3Result, extraArgs, reference);
     }
@@ -151,7 +149,7 @@ private void assertVariantContextsMatch(List<File> inputs, File expected, List<S
     }
 
     public void runCombineGVCFSandAssertSomething(List<File> inputs, File expected, List<String> additionalArguments, BiConsumer<VariantContext, VariantContext> assertion, String reference) throws IOException {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(reference))
@@ -195,7 +193,7 @@ private static VCFHeader getHeaderFromFile(final File vcfFile) throws IOExceptio
 
     @Test
     public void testOneStartsBeforeTwoAndEndsAfterwards() throws Exception {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
@@ -227,7 +225,7 @@ public void testOneStartsBeforeTwoAndEndsAfterwards() throws Exception {
 
     @Test()
     public void testTetraploidRun() throws IOException {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
@@ -248,7 +246,7 @@ public void testTetraploidRun() throws IOException {
 
     @Test
     public void testTwoSpansManyBlocksInOne() throws Exception {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
@@ -267,7 +265,7 @@ public void testTwoSpansManyBlocksInOne() throws Exception {
     // Ensuring that no exception is thrown and that the resulting VCF is empty
     @Test
     public void testNoDataInInterval() throws Exception {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
@@ -286,7 +284,7 @@ public void testNoDataInInterval() throws Exception {
 
     @Test
     public void testOneHasAltAndTwoHasNothing() throws Exception {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
@@ -307,7 +305,7 @@ public void testOneHasAltAndTwoHasNothing() throws Exception {
 
     @Test
     public void testOneHasAltAndTwoHasRefBlock() throws Exception {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
@@ -332,7 +330,7 @@ public void testOneHasAltAndTwoHasRefBlock() throws Exception {
 
     @Test
     public void testOneHasDeletionAndTwoHasRefBlock() throws Exception {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
@@ -369,7 +367,7 @@ public void testOneHasDeletionAndTwoHasRefBlock() throws Exception {
     // This test asserts that the behavior is rational in the case of whole genome gvcfs which have variants starting at
     // the first and ending on the last base of each contig.
     public void testStartChromosome() throws Exception {
-        final File output = createTempFile("genotypegvcf", ".vcf");
+        final File output = createTempFile("combinegvcfs", ".vcf");
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(b37_reference_20_21))
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfExample1WithTrailingReferenceBlocks.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfExample1WithTrailingReferenceBlocks.g.vcf
new file mode 100644
index 00000000000..ec5f33cf951
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfExample1WithTrailingReferenceBlocks.g.vcf
@@ -0,0 +1,47 @@
+##fileformat=VCFv4.1
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive)
+##INFO=<ID=BLOCK_SIZE,Number=1,Type=Integer,Description="Size of the homozygous reference GVCF block">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##contig=<ID=chr20,length=64444167>
+##contig=<ID=chr21,length=46709983>
+##contig=<ID=chr20_GL383577v2_alt,length=128386>
+##contig=<ID=chr20_KI270869v1_alt,length=118774>
+##contig=<ID=chr20_KI270871v1_alt,length=58661>
+##contig=<ID=chr20_KI270870v1_alt,length= 183433>
+##contig=<ID=chr21_GL383578v2_alt,length=63917>
+##contig=<ID=chr21_KI270874v1_alt,length= 166743>
+##contig=<ID=chr21_KI270873v1_alt,length=143900>
+##contig=<ID=chr21_GL383579v2_alt,length=201197>
+##contig=<ID=chr21_GL383580v2_alt,length=74653>
+##contig=<ID=chr21_GL383581v2_alt,length=116689>
+##contig=<ID=chr21_KI270872v1_alt,length=82692>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1
+chr20	69491	.	G	<NON_REF>	.	.	BLOCK_SIZE=20;END=69510	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:94:99:82:99:0,120,1800
+chr20	69511	.	A	G,<NON_REF>	2253.77	.	BaseQRankSum=1.169;DP=82;MQ=31.05;MQ0=0;MQRankSum=-0.866;ReadPosRankSum=1.689	GT:AD:DP:GQ:PL:SB	1/1:1,79,0:80:99:2284,207,0,2287,237,2316:0,1,46,33
+chr20	69512	.	C	<NON_REF>	.	.	BLOCK_SIZE=10;END=69521	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:96:99:82:99:0,120,1800
+chr20	69522	.	T	<NON_REF>	.	.	BLOCK_SIZE=27;END=69548	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:95:0:95:0:0,0,0
+chr20	69549	.	G	<NON_REF>	.	.	BLOCK_SIZE=86;END=69634	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:156:99:56:66:0,66,990
+chr20	69635	.	G	T,<NON_REF>	60.77	.	BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRankSum=1.300;ReadPosRankSum=1.754	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:89:89,0,119,101,128,229:0,4,0,3
+chr20	69762	.	T	<NON_REF>	.	.	BLOCK_SIZE=1;END=69762	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:18:7:18:0,18,270
+chr20	69763	.	A	<NON_REF>	.	.	BLOCK_SIZE=4;END=69766	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:21:7:21:0,21,253
+chr20	69767	.	C	<NON_REF>	.	.	BLOCK_SIZE=5;END=69771	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:12:7:12:0,12,180
+chr20	69772	.	AAAGC	A,<NON_REF>	60.77	.	BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRankSum=1.300;ReadPosRankSum=1.754	GT:AD:DP:GQ:PL:SB	0/1:4,3,0:7:89:89,0,119,101,128,229:0,4,0,3
+chr20	69773	.	A	<NON_REF>	.	.	BLOCK_SIZE=10;END=69783	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:0:3:0:0,0,0
+chr21	1	.	G	<NON_REF>	.	.	END=46709983	GT:DP:GQ:MIN_DP:PL	0/0:0:0:0:0,0,0
+chr20_GL383577v2_alt	1	.	G	<NON_REF>	.	.	END=128386	GT:DP:GQ:MIN_DP:PL	0/0:0:0:0:0,0,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfExample2WithTrailingReferenceBlocks.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfExample2WithTrailingReferenceBlocks.g.vcf
new file mode 100644
index 00000000000..b3ad4bcb99c
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfExample2WithTrailingReferenceBlocks.g.vcf
@@ -0,0 +1,41 @@
+##fileformat=VCFv4.1
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive)
+##INFO=<ID=BLOCK_SIZE,Number=1,Type=Integer,Description="Size of the homozygous reference GVCF block">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##contig=<ID=chr20,length=64444167>
+##contig=<ID=chr21,length=46709983>
+##contig=<ID=chr20_GL383577v2_alt,length=128386>
+##contig=<ID=chr20_KI270869v1_alt,length=118774>
+##contig=<ID=chr20_KI270871v1_alt,length=58661>
+##contig=<ID=chr20_KI270870v1_alt,length= 183433>
+##contig=<ID=chr21_GL383578v2_alt,length=63917>
+##contig=<ID=chr21_KI270874v1_alt,length= 166743>
+##contig=<ID=chr21_KI270873v1_alt,length=143900>
+##contig=<ID=chr21_GL383579v2_alt,length=201197>
+##contig=<ID=chr21_GL383580v2_alt,length=74653>
+##contig=<ID=chr21_GL383581v2_alt,length=116689>
+##contig=<ID=chr21_KI270872v1_alt,length=82692>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA2
+chr20	69498	.	C	<NON_REF>	.	.	BLOCK_SIZE=9;END=69506	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:94:99:82:99:0,120,1800
+chr20	69514	.	T	<NON_REF>	.	.	BLOCK_SIZE=111;END=69624	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:96:99:82:99:0,120,1800
+chr20	69625	.	A	<NON_REF>	.	.	BLOCK_SIZE=51;END=69675	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:18:7:18:0,18,270
+chr20	69767	.	C	<NON_REF>	.	.	BLOCK_SIZE=8;END=69774	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:12:7:15:0,12,180
+chr20	69775	.	C	<NON_REF>	.	.	BLOCK_SIZE=17;END=69791	GT:DP:GQ:MIN_DP:MIN_GQ:PL	0/0:7:15:7:15:0,15,160
+chr21	1	.	G	<NON_REF>	.	.	END=46709983	GT:DP:GQ:MIN_DP:PL	0/0:0:0:0:0,0,0
+chr20_GL383577v2_alt	1	.	G	<NON_REF>	.	.	END=128386	GT:DP:GQ:MIN_DP:PL	0/0:0:0:0:0,0,0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf
new file mode 100644
index 00000000000..a041b98c6d9
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf
@@ -0,0 +1,65 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs  --output /var/folders/cr/16ghvyfj5lvfwxx01rt1k4tdl04sy3/T/combinegvcfs3876000008240987478.vcf --variant /Users/cnorman/projects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfExample1WithTrailingReferenceBlocks.g.vcf --variant /Users/cnorman/projects/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfExample2WithTrailingReferenceBlocks.g.vcf --reference /Users/cnorman/projects/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta --verbosity ERROR  --annotation-group StandardAnnotation --disable-tool-default-annotations false --convert-to-base-pair-resolution false --break-bands-at-multiples-of 0 --ignore-variants-starting-outside-interval false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=Unavailable,Date="March 29, 2018 6:17:47 PM EDT">
+##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive)
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BLOCK_SIZE,Number=1,Type=Integer,Description="Size of the homozygous reference GVCF block">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##contig=<ID=chr20,length=64444167>
+##contig=<ID=chr21,length=46709983>
+##contig=<ID=chr20_GL383577v2_alt,length=128386>
+##contig=<ID=chr20_KI270869v1_alt,length=118774>
+##contig=<ID=chr20_KI270871v1_alt,length=58661>
+##contig=<ID=chr20_KI270870v1_alt,length=183433>
+##contig=<ID=chr21_GL383578v2_alt,length=63917>
+##contig=<ID=chr21_KI270874v1_alt,length=166743>
+##contig=<ID=chr21_KI270873v1_alt,length=143900>
+##contig=<ID=chr21_GL383579v2_alt,length=201197>
+##contig=<ID=chr21_GL383580v2_alt,length=74653>
+##contig=<ID=chr21_GL383581v2_alt,length=116689>
+##contig=<ID=chr21_KI270872v1_alt,length=82692>
+##source=CombineGVCFs
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1	NA2
+chr20	69491	.	G	<NON_REF>	.	.	END=69497	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:94:99:82:99:0,120,1800	./.
+chr20	69498	.	C	<NON_REF>	.	.	END=69506	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:94:99:82:99:0,120,1800	./.:94:99:82:99:0,120,1800
+chr20	69507	.	T	<NON_REF>	.	.	END=69510	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:94:99:82:99:0,120,1800	./.
+chr20	69511	.	A	G,<NON_REF>	.	.	BaseQRankSum=1.17;DP=82;MQ=31.05;MQ0=0;MQRankSum=-8.660e-01;ReadPosRankSum=1.69	GT:AD:DP:GQ:PL:SB	./.:1,79,0:80:99:2284,207,0,2287,237,2316:0,1,46,33	./.
+chr20	69512	.	C	<NON_REF>	.	.	END=69513	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:96:99:82:99:0,120,1800	./.
+chr20	69514	.	T	<NON_REF>	.	.	END=69521	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:96:99:82:99:0,120,1800	./.:96:99:82:99:0,120,1800
+chr20	69522	.	T	<NON_REF>	.	.	END=69548	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:95:0:95:0:0,0,0	./.:96:99:82:99:0,120,1800
+chr20	69549	.	G	<NON_REF>	.	.	END=69624	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:156:99:56:66:0,66,990	./.:96:99:82:99:0,120,1800
+chr20	69625	.	A	<NON_REF>	.	.	END=69634	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:156:99:56:66:0,66,990	./.:7:18:7:18:0,18,270
+chr20	69635	.	G	T,<NON_REF>	.	.	BaseQRankSum=0.937;DP=14;MQ=34.15;MQ0=0;MQRankSum=1.30;ReadPosRankSum=1.75	GT:AD:DP:GQ:MIN_DP:MIN_GQ:PL:SB	./.:4,3,0:7:89:.:.:89,0,119,101,128,229:0,4,0,3	./.:.:7:18:7:18:0,18,270,18,270,270
+chr20	69636	.	A	<NON_REF>	.	.	END=69675	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.	./.:7:18:7:18:0,18,270
+chr20	69762	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:7:18:7:18:0,18,270	./.
+chr20	69763	.	A	<NON_REF>	.	.	END=69766	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:7:21:7:21:0,21,253	./.
+chr20	69767	.	C	<NON_REF>	.	.	END=69771	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:7:12:7:12:0,12,180	./.:7:12:7:15:0,12,180
+chr20	69772	.	AAAGC	A,<NON_REF>	.	.	BaseQRankSum=0.937;DP=14;MQ=34.15;MQ0=0;MQRankSum=1.30;ReadPosRankSum=1.75	GT:AD:DP:GQ:MIN_DP:MIN_GQ:PL:SB	./.:4,3,0:7:89:.:.:89,0,119,101,128,229:0,4,0,3	./.:.:7:12:7:15:0,12,180,12,180,180
+chr20	69773	.	A	<NON_REF>	.	.	END=69774	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:7:0:3:0:0,0,0	./.:7:12:7:15:0,12,180
+chr20	69775	.	C	<NON_REF>	.	.	END=69783	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.:7:0:3:0:0,0,0	./.:7:15:7:15:0,15,160
+chr20	69784	.	A	<NON_REF>	.	.	END=69791	GT:DP:GQ:MIN_DP:MIN_GQ:PL	./.	./.:7:15:7:15:0,15,160
+chr21	1	.	G	<NON_REF>	.	.	END=46709983	GT:DP:GQ:MIN_DP:PL	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0
+chr20_GL383577v2_alt	1	.	G	<NON_REF>	.	.	END=128386	GT:DP:GQ:MIN_DP:PL	./.:0:0:0:0,0,0	./.:0:0:0:0,0,0