diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java
index 532ecd59cd0..09a9aba30b2 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java
@@ -37,44 +37,50 @@ public Object[][] getVCFdata() {
                 // Simple Test, spanning deletions; standard calling confidence
                 //No variants outside requested intervals; no SNPs with QUAL < 60, no INDELs with QUAL < 69?; has star alleles after deletion at chr20:263497; has AC, AF, AN, DP, ExcessHet, FS, MQ, (MQRankSum), (ReadPosRankSum), SOR, QD; has called genotypes
                  {new File[]{getTestFile("sample1.vcf"), getTestFile("sample2.vcf"), getTestFile("sample3.vcf"), getTestFile("sample4.vcf"), getTestFile("sample5.vcf")},
-                         getTestFile("fiveSampleTest.vcf"), Arrays.asList(new SimpleInterval("chr20", 251370, 252000), new SimpleInterval("chr20", 263000, 265600)), Arrays.asList("--merge-input-intervals", "--only-output-calls-starting-in-intervals"), b38_reference_20_21},
+                         getTestFile("fiveSampleTest.vcf"), null, Arrays.asList(new SimpleInterval("chr20", 251370, 252000), new SimpleInterval("chr20", 263000, 265600)), Arrays.asList("--merge-input-intervals", "--only-output-calls-starting-in-intervals"), b38_reference_20_21},
 
                 //lower calling confidence
                 //same as above except (different intervals and) with SNPs with 40 < QUAL < 60 and INDELs with 49 < QUAL < 69
                 {new File[]{getTestFile("sample1.vcf"), getTestFile("sample2.vcf"), getTestFile("sample3.vcf"), getTestFile("sample4.vcf"), getTestFile("sample5.vcf")},
-                         getTestFile("fiveSampleTest.lowerCallThreshold.vcf"), Arrays.asList(new SimpleInterval("chr20", 250865, 348163)), Arrays.asList("-stand-call-conf 10"), b38_reference_20_21},
+                         getTestFile("fiveSampleTest.lowerCallThreshold.vcf"), null, Arrays.asList(new SimpleInterval("chr20", 250865, 348163)), Arrays.asList("-stand-call-conf 10"), b38_reference_20_21},
 
                 //using latest reblocking output with allele-specific annotations
                 //has all of the above plus AS_AltDP, AS_FS, AS_MQ, AS_MQRankSum, AS_QD, AS_ReadPosRankSum
                 {new File[]{new File(getToolTestDataDir() + "/../variantutils/ReblockGVCF/expected.NA12878.AS.chr20snippet.reblocked.g.vcf"),
                          new File(getToolTestDataDir() + "/../variantutils/ReblockGVCF/expected.NA12892.AS.chr20snippet.reblocked.g.vcf")},
-                         getTestFile("twoSampleAS.vcf"), Arrays.asList(new SimpleInterval("20")), NO_EXTRA_ARGS, b37_reference_20_21},
+                         getTestFile("twoSampleAS.vcf"), getTestFile("twoSampleASDB.vcf"), Arrays.asList(new SimpleInterval("20")), NO_EXTRA_ARGS, b37_reference_20_21},
 
                 //using legacy reblocking data with no raw GT count values
                 //has ExcessHet, calculated from genotypes
                 {new File[]{new File(getToolTestDataDir() + "noGTCount.sample1.chr20snippet.vcf"),
                         new File(getToolTestDataDir() + "noGTCount.sample2.chr20snippet.vcf")},
-                        getTestFile("noGTCount.expected.chr20snippet.vcf"), Arrays.asList(new SimpleInterval("chr20")), NO_EXTRA_ARGS, hg38Reference
+                        getTestFile("noGTCount.expected.chr20snippet.vcf"), null, Arrays.asList(new SimpleInterval("chr20")), NO_EXTRA_ARGS, hg38Reference
                 }
         };
     }
 
 
     @Test (dataProvider = "VCFdata")
-    public void testUsingGenomicsDB(File[] inputs, File expected, List<SimpleInterval> intervals, List<String> additionalArguments, String reference) throws IOException {
+    public void testUsingGenomicsDB(File[] inputs, File expected, File expectedDb, List<SimpleInterval> intervals, List<String> additionalArguments, String reference) throws IOException {
         final File tempGenomicsDB = GenomicsDBTestUtils.createTempGenomicsDB(Arrays.asList(inputs), IntervalUtils.getSpanningInterval(intervals));
         final String genomicsDBUri = GenomicsDBTestUtils.makeGenomicsDBUri(tempGenomicsDB);
 
-        File output = runTool(genomicsDBUri, intervals, reference, additionalArguments);
+        final File output = createTempFile("GnarlyGenotyper", ".vcf");
+        final File outputDatabase = createTempFile("GnarlyGenotyper.annotationDatabase", ".vcf");
+
+        runTool(genomicsDBUri, intervals, reference, output, outputDatabase, additionalArguments);
 
         final List<VariantContext> expectedVC = getVariantContexts(expected);
         final List<VariantContext> actualVC = getVariantContexts(output);
         VariantContextTestUtils.assertEqualVariants(actualVC, expectedVC);
+        if (expectedDb != null) {
+            final List<VariantContext> expectedDB = getVariantContexts(expectedDb);
+            final List<VariantContext> actualDB = getVariantContexts(outputDatabase);
+            VariantContextTestUtils.assertEqualVariants(actualDB, expectedDB);
+        }
     }
 
-    protected File runTool(String input, List<SimpleInterval> intervals, String reference, List<String> additionalArguments) {
-        final File output = createTempFile("GnarlyGenotyper", ".vcf");
-        final File outputDatabase = createTempFile("GnarlyGenotyper.annotationDatabase", ".vcf");
+    protected void runTool(String input, List<SimpleInterval> intervals, String reference, File output, File outputDatabase, List<String> additionalArguments) {
 
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addReference(new File(reference))
@@ -86,7 +92,6 @@ protected File runTool(String input, List<SimpleInterval> intervals, String refe
         additionalArguments.forEach(args::add);
 
         runCommandLine(args);
-        return output;
     }
 
     @Test
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf
new file mode 100644
index 00000000000..4bece06d4cb
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf
@@ -0,0 +1,167 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##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=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##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.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-43-gc7dbd4f,Date="Tue Jun 27 08:39:50 EDT 2017",Epoch=1498567190652,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/Users/gauthier/workspaces/gsa-unstable/private/gatk-tools-private/src/test/resources//NA12878.HiSeq.b37.chr20.10_11mb.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[20:10433000-10437000, 20:10087820, 20:10684106] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[Standard, AS_Standard] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport  --genomicsdb-workspace-path /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsDBWorkspace4126760032453666467/workspace --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/../variantutils/ReblockGVCF/expected.NA12878.AS.chr20snippet.reblocked.g.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/../variantutils/ReblockGVCF/expected.NA12892.AS.chr20snippet.reblocked.g.vcf --intervals 20:1-2147483647 --verbosity ERROR  --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --batch-size 0 --consolidate false --validate-sample-name-map false --merge-input-intervals false --reader-threads 1 --max-num-intervals-to-import-in-parallel 1 --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 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="Unavailable",Date="July 22, 2019 4:18:00 PM EDT">
+##GATKCommandLine=<ID=GnarlyGenotyper,CommandLine="GnarlyGenotyper  --output /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/GnarlyGenotyper760124483387681187.vcf --output-database-name /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/GnarlyGenotyper.annotationDatabase7661556228301376823.vcf --variant gendb:///var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsDBWorkspace4126760032453666467/workspace --intervals 20:1-2147483647 --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta --verbosity ERROR  --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --keep-all-sites false --only-output-calls-starting-in-intervals false --merge-input-intervals false --strip-allele-specific-annotations 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 --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="Unavailable",Date="July 22, 2019 4:18:00 PM EDT">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_adj,Number=A,Type=Integer,Description="Allele count for each ALT, adjusted to represent high quality genotypes only">
+##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=AS_AltDP,Number=A,Type=Integer,Description="Allele-specific (informative) depth for alt alleles over variant genotypes; effectively sum of ADs">
+##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
+##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient">
+##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
+##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
+##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
+##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
+##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities">
+##INFO=<ID=AS_RAW_MQ,Number=1,Type=String,Description="Allele-specfic raw data for RMS Mapping Quality">
+##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specific raw data for Mapping Quality Rank Sum">
+##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias">
+##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
+##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests">
+##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
+##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format">
+##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=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=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity">
+##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SB_TABLE,Number=4,Type=Integer,Description="Forward/reverse read counts for strand bias tests">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
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+##contig=<ID=GL000217.1,length=172149>
+##contig=<ID=GL000216.1,length=172294>
+##contig=<ID=GL000215.1,length=172545>
+##contig=<ID=GL000205.1,length=174588>
+##contig=<ID=GL000219.1,length=179198>
+##contig=<ID=GL000224.1,length=179693>
+##contig=<ID=GL000223.1,length=180455>
+##contig=<ID=GL000195.1,length=182896>
+##contig=<ID=GL000212.1,length=186858>
+##contig=<ID=GL000222.1,length=186861>
+##contig=<ID=GL000200.1,length=187035>
+##contig=<ID=GL000193.1,length=189789>
+##contig=<ID=GL000194.1,length=191469>
+##contig=<ID=GL000225.1,length=211173>
+##contig=<ID=GL000192.1,length=547496>
+##contig=<ID=NC_007605,length=171823>
+##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
+##source=GenomicsDBImport
+##source=GnarlyGenotyper
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	10087820	.	C	CAG,CAGAGAG	.	.	AC=1,1;AF=0.250,0.250;AN=4;AS_QUALapprox=|302|606|0;AS_RAW_BaseQRankSum=|-2.100,1|1.000,1|;AS_RAW_MQ=220977.000|46800.000|47258.000|0.000;AS_RAW_MQRankSum=|0.600,1|-3.100,1|;AS_RAW_ReadPosRankSum=|-0.400,1|-0.300,1|;AS_SB_TABLE=33,31|8,5|12,12|0,0;AS_VarDP=64|13|24|0;BaseQRankSum=0.955;DP=167;MQRankSum=0.678;MQ_DP=167;QUALapprox=908;RAW_GT_COUNT=0,2,0;RAW_MQ=541599.00;RAW_MQandDP=541599,167;ReadPosRankSum=-2.540e-01;SB_TABLE=33,31,21,19;VarDP=104
+20	10433322	.	A	AT	.	.	AC=2;AF=0.500;AN=4;AS_QUALapprox=|574|0;AS_RAW_BaseQRankSum=|0.800,1,2.500,1|;AS_RAW_MQ=17782.000|41312.000|0.000;AS_RAW_MQRankSum=|1.100,1,2.200,1|;AS_RAW_ReadPosRankSum=|1.900,1,2.000,1|;AS_SB_TABLE=7,8|8,9|0,0;AS_VarDP=15|17|0;BaseQRankSum=2.56;DP=77;MQRankSum=1.89;MQ_DP=77;QUALapprox=574;RAW_GT_COUNT=0,2,0;RAW_MQ=154528.00;RAW_MQandDP=154528,77;ReadPosRankSum=2.04;SB_TABLE=7,8,10,10;VarDP=35
+20	10433324	.	A	T	.	.	AC=3;AF=0.750;AN=4;AS_QUALapprox=|1105|0;AS_RAW_BaseQRankSum=|2.200,1|;AS_RAW_MQ=12736.000|48881.000|0.000;AS_RAW_MQRankSum=|0.500,1|;AS_RAW_ReadPosRankSum=|1.500,1|;AS_SB_TABLE=2,7|13,13|0,0;AS_VarDP=9|26|0;BaseQRankSum=2.28;DP=73;MQRankSum=0.871;MQ_DP=73;QUALapprox=1105;RAW_GT_COUNT=0,1,1;RAW_MQ=140128.00;RAW_MQandDP=140128,73;ReadPosRankSum=1.74;SB_TABLE=2,7,13,13;VarDP=35
+20	10433326	.	A	T	.	.	AC=3;AF=0.750;AN=4;AS_QUALapprox=|1105|0;AS_RAW_BaseQRankSum=|0.800,1|;AS_RAW_MQ=12736.000|48881.000|0.000;AS_RAW_MQRankSum=|0.500,1|;AS_RAW_ReadPosRankSum=|1.400,1|;AS_SB_TABLE=2,7|13,13|0,0;AS_VarDP=9|26|0;BaseQRankSum=1.54;DP=67;MQRankSum=0.871;MQ_DP=67;QUALapprox=1105;RAW_GT_COUNT=0,1,1;RAW_MQ=118528.00;RAW_MQandDP=118528,67;ReadPosRankSum=1.74;SB_TABLE=2,7,13,13;VarDP=35
+20	10433328	.	A	T,ATATAT	.	.	AC=3,1;AF=0.750,0.250;AN=4;AS_QUALapprox=|1933|499|0;AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.000|48881.000|2523.000|0.000;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|13,13|1,2|0,0;AS_VarDP=0|26|3|0;DP=66;MQ_DP=66;QUALapprox=2110;RAW_GT_COUNT=0,0,2;RAW_MQ=114928.00;RAW_MQandDP=114928,66;SB_TABLE=0,0,14,15;VarDP=29
+20	10433382	.	T	C	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|632|0;AS_RAW_BaseQRankSum=|-1.900,1|;AS_RAW_MQ=40862.000|45723.000|0.000;AS_RAW_MQRankSum=|1.000,1|;AS_RAW_ReadPosRankSum=|0.200,1|;AS_SB_TABLE=10,5|11,4|0,0;AS_VarDP=15|15|0;BaseQRankSum=-1.821e+00;DP=55;MQRankSum=1.03;MQ_DP=30;QUALapprox=632;RAW_GT_COUNT=0,1,0;RAW_MQ=86585.00;RAW_MQandDP=86585,30;ReadPosRankSum=0.249;SB_TABLE=10,5,11,4;VarDP=30
+20	10433391	.	T	C	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|631|0;AS_RAW_BaseQRankSum=|-0.300,1|;AS_RAW_MQ=51662.000|52082.000|0.000;AS_RAW_MQRankSum=|1.300,1|;AS_RAW_ReadPosRankSum=|1.500,1|;AS_SB_TABLE=14,4|13,3|0,0;AS_VarDP=18|16|0;BaseQRankSum=-2.840e-01;DP=59;MQRankSum=1.33;MQ_DP=34;QUALapprox=631;RAW_GT_COUNT=0,1,0;RAW_MQ=103744.00;RAW_MQandDP=103744,34;ReadPosRankSum=1.54;SB_TABLE=14,4,13,3;VarDP=34
+20	10433468	.	T	C	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|653|0;AS_RAW_BaseQRankSum=|-1.400,1|;AS_RAW_MQ=63049.000|69241.000|0.000;AS_RAW_MQRankSum=|0.000,1|;AS_RAW_ReadPosRankSum=|1.400,1|;AS_SB_TABLE=13,5|12,8|0,0;AS_VarDP=18|20|0;BaseQRankSum=-1.312e+00;DP=63;MQRankSum=0.076;MQ_DP=38;QUALapprox=653;RAW_GT_COUNT=0,1,0;RAW_MQ=132290.00;RAW_MQandDP=132290,38;ReadPosRankSum=1.46;SB_TABLE=13,5,12,8;VarDP=38
+20	10433560	.	C	A	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|995|0;AS_RAW_BaseQRankSum=|3.400,1|;AS_RAW_MQ=111600.000|87769.000|0.000;AS_RAW_MQRankSum=|-1.100,1|;AS_RAW_ReadPosRankSum=|1.300,1|;AS_SB_TABLE=30,1|22,3|0,0;AS_VarDP=31|25|0;BaseQRankSum=3.50;DP=81;MQRankSum=-1.078e+00;MQ_DP=56;QUALapprox=995;RAW_GT_COUNT=0,1,0;RAW_MQ=199369.00;RAW_MQandDP=199369,56;ReadPosRankSum=1.38;SB_TABLE=30,1,22,3;VarDP=56
+20	10433575	.	C	T	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1151|0;AS_RAW_BaseQRankSum=|3.800,1|;AS_RAW_MQ=119641.000|100251.000|0.000;AS_RAW_MQRankSum=|-1.200,1|;AS_RAW_ReadPosRankSum=|0.800,1|;AS_SB_TABLE=31,3|26,4|0,0;AS_VarDP=34|30|0;BaseQRankSum=3.81;DP=89;MQRankSum=-1.123e+00;MQ_DP=64;QUALapprox=1151;RAW_GT_COUNT=0,1,0;RAW_MQ=219892.00;RAW_MQandDP=219892,64;ReadPosRankSum=0.830;SB_TABLE=31,3,26,4;VarDP=64
+20	10433594	.	C	T	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1113|0;AS_RAW_BaseQRankSum=|4.800,1|;AS_RAW_MQ=108841.000|85615.000|0.000;AS_RAW_MQRankSum=|-2.400,1|;AS_RAW_ReadPosRankSum=|-0.600,1|;AS_SB_TABLE=28,3|25,4|0,0;AS_VarDP=31|29|0;BaseQRankSum=4.82;DP=86;MQRankSum=-2.334e+00;MQ_DP=61;QUALapprox=1113;RAW_GT_COUNT=0,1,0;RAW_MQ=195825.00;RAW_MQandDP=195825,61;ReadPosRankSum=-5.020e-01;SB_TABLE=28,3,25,4;VarDP=60
+20	10433809	.	A	G	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1143|0;AS_RAW_BaseQRankSum=|1.400,1|;AS_RAW_MQ=115200.000|122400.000|0.000;AS_RAW_MQRankSum=|0.000,1|;AS_RAW_ReadPosRankSum=|-0.500,1|;AS_SB_TABLE=13,19|12,22|0,0;AS_VarDP=32|34|0;BaseQRankSum=1.40;DP=93;MQRankSum=0.00;MQ_DP=68;QUALapprox=1143;RAW_GT_COUNT=0,1,0;RAW_MQ=242569.00;RAW_MQandDP=242569,68;ReadPosRankSum=-4.450e-01;SB_TABLE=13,19,12,22;VarDP=66
+20	10433955	.	C	CGTGTGTGTGTAT	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1035|0;AS_RAW_BaseQRankSum=|0.400,1|;AS_RAW_MQ=59810.000|39497.000|0.000;AS_RAW_MQRankSum=|-4.000,1|;AS_RAW_ReadPosRankSum=|-0.800,1|;AS_SB_TABLE=12,6|16,8|0,0;AS_VarDP=18|24|0;BaseQRankSum=0.422;DP=72;MQRankSum=-4.001e+00;MQ_DP=47;QUALapprox=1035;RAW_GT_COUNT=0,1,0;RAW_MQ=117307.00;RAW_MQandDP=117307,47;ReadPosRankSum=-7.890e-01;SB_TABLE=12,6,16,8;VarDP=42
+20	10434177	.	A	T	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1475|0;AS_RAW_BaseQRankSum=|0.900,1|;AS_RAW_MQ=108000.000|133784.000|0.000;AS_RAW_MQRankSum=|-2.500,1|;AS_RAW_ReadPosRankSum=|-0.900,1|;AS_SB_TABLE=15,15|23,20|0,0;AS_VarDP=30|43|0;BaseQRankSum=0.903;DP=99;MQRankSum=-2.473e+00;MQ_DP=74;QUALapprox=1475;RAW_GT_COUNT=0,1,0;RAW_MQ=245384.00;RAW_MQandDP=245384,74;ReadPosRankSum=-8.910e-01;SB_TABLE=15,15,23,20;VarDP=73
+20	10434258	.	G	A	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1243|0;AS_RAW_BaseQRankSum=|3.000,1|;AS_RAW_MQ=109369.000|106451.000|0.000;AS_RAW_MQRankSum=|-2.900,1|;AS_RAW_ReadPosRankSum=|-0.200,1|;AS_SB_TABLE=19,12|24,14|0,0;AS_VarDP=31|38|0;BaseQRankSum=3.06;DP=95;MQRankSum=-2.871e+00;MQ_DP=70;QUALapprox=1243;RAW_GT_COUNT=0,1,0;RAW_MQ=219420.00;RAW_MQandDP=219420,70;ReadPosRankSum=-1.550e-01;SB_TABLE=19,12,24,14;VarDP=69
+20	10434384	.	TA	T	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|790|0;AS_RAW_BaseQRankSum=|-0.100,1|;AS_RAW_MQ=123769.000|118800.000|0.000;AS_RAW_MQRankSum=|1.000,1|;AS_RAW_ReadPosRankSum=|0.400,1|;AS_SB_TABLE=22,13|21,12|0,0;AS_VarDP=35|33|0;BaseQRankSum=-1.000e-01;DP=96;MQRankSum=1.00;MQ_DP=71;QUALapprox=790;RAW_GT_COUNT=0,1,0;RAW_MQ=253369.00;RAW_MQandDP=253369,71;ReadPosRankSum=0.497;SB_TABLE=22,13,21,12;VarDP=68
+20	10434519	.	T	C	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1472|0;AS_RAW_BaseQRankSum=|-3.200,1|;AS_RAW_MQ=126000.000|154800.000|0.000;AS_RAW_MQRankSum=|0.000,1|;AS_RAW_ReadPosRankSum=|-0.800,1|;AS_SB_TABLE=18,17|19,24|0,0;AS_VarDP=35|43|0;BaseQRankSum=-3.137e+00;DP=103;MQRankSum=0.00;MQ_DP=78;QUALapprox=1472;RAW_GT_COUNT=0,1,0;RAW_MQ=280800.00;RAW_MQandDP=280800,78;ReadPosRankSum=-7.490e-01;SB_TABLE=18,17,19,24;VarDP=78
+20	10435067	.	GTA	G	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1454|0;AS_RAW_BaseQRankSum=|2.600,1|;AS_RAW_MQ=108000.000|133200.000|0.000;AS_RAW_MQRankSum=|0.000,1|;AS_RAW_ReadPosRankSum=|-0.200,1|;AS_SB_TABLE=15,15|22,15|0,0;AS_VarDP=30|37|0;BaseQRankSum=2.60;DP=92;MQRankSum=0.00;MQ_DP=67;QUALapprox=1454;RAW_GT_COUNT=0,1,0;RAW_MQ=241200.00;RAW_MQandDP=241200,67;ReadPosRankSum=-1.830e-01;SB_TABLE=15,15,22,15;VarDP=67
+20	10435948	.	A	C	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1145|0;AS_RAW_BaseQRankSum=|-4.700,1|;AS_RAW_MQ=144000.000|107528.000|0.000;AS_RAW_MQRankSum=|-3.200,1|;AS_RAW_ReadPosRankSum=|-1.600,1|;AS_SB_TABLE=19,21|20,16|0,0;AS_VarDP=40|36|0;BaseQRankSum=-4.692e+00;DP=101;MQRankSum=-3.121e+00;MQ_DP=76;QUALapprox=1145;RAW_GT_COUNT=0,1,0;RAW_MQ=251528.00;RAW_MQandDP=251528,76;ReadPosRankSum=-1.594e+00;SB_TABLE=19,21,20,16;VarDP=76
+20	10436227	.	TTTTATTTATTTATTTATTTA	T,TTTTATTTATTTATTTATTTATTTA	.	.	AC=1,3;AF=0.250,0.750;AN=4;AS_QUALapprox=|984|703|0;AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=3600.000|25702.000|48876.000|0.000;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=1,0|14,10|11,6|0,0;AS_VarDP=1|24|17|0;BaseQRankSum=-1.450e+00;DP=108;MQRankSum=-1.660e+00;MQ_DP=108;QUALapprox=1650;RAW_GT_COUNT=0,0,2;RAW_MQ=313019.00;RAW_MQandDP=313019,108;ReadPosRankSum=1.30;SB_TABLE=1,0,25,16;VarDP=42
+20	10436415	.	A	G	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1198|0;AS_RAW_BaseQRankSum=|-2.800,1|;AS_RAW_MQ=81904.000|141241.000|0.000;AS_RAW_MQRankSum=|0.400,1|;AS_RAW_ReadPosRankSum=|-0.100,1|;AS_SB_TABLE=15,8|17,23|0,0;AS_VarDP=23|40|0;BaseQRankSum=-2.775e+00;DP=87;MQRankSum=0.399;MQ_DP=63;QUALapprox=1198;RAW_GT_COUNT=0,1,0;RAW_MQ=223145.00;RAW_MQandDP=223145,63;ReadPosRankSum=-6.300e-02;SB_TABLE=15,8,17,23;VarDP=63
+20	10436582	.	A	G	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1195|0;AS_RAW_BaseQRankSum=|-1.400,1|;AS_RAW_MQ=117410.000|103379.000|0.000;AS_RAW_MQRankSum=|-2.700,1|;AS_RAW_ReadPosRankSum=|0.200,1|;AS_SB_TABLE=16,18|21,16|0,0;AS_VarDP=34|37|0;BaseQRankSum=-1.326e+00;DP=95;MQRankSum=-2.639e+00;MQ_DP=71;QUALapprox=1195;RAW_GT_COUNT=0,1,0;RAW_MQ=220789.00;RAW_MQandDP=220789,71;ReadPosRankSum=0.267;SB_TABLE=16,18,21,16;VarDP=71
+20	10436700	.	A	G	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1341|0;AS_RAW_BaseQRankSum=|-1.400,1|;AS_RAW_MQ=108000.000|141769.000|0.000;AS_RAW_MQRankSum=|-0.900,1|;AS_RAW_ReadPosRankSum=|0.500,1|;AS_SB_TABLE=18,12|21,19|0,0;AS_VarDP=30|40|0;BaseQRankSum=-1.329e+00;DP=94;MQRankSum=-8.370e-01;MQ_DP=70;QUALapprox=1341;RAW_GT_COUNT=0,1,0;RAW_MQ=249769.00;RAW_MQandDP=249769,70;ReadPosRankSum=0.581;SB_TABLE=18,12,21,19;VarDP=70
+20	10436908	.	C	G	.	.	AC=1;AF=0.250;AN=4;AS_QUALapprox=|1369|0;AS_RAW_BaseQRankSum=|-0.900,1|;AS_RAW_MQ=145849.000|145638.000|0.000;AS_RAW_MQRankSum=|-1.000,1|;AS_RAW_ReadPosRankSum=|-0.200,1|;AS_SB_TABLE=15,26|11,31|0,0;AS_VarDP=41|42|0;BaseQRankSum=-8.440e-01;DP=107;MQRankSum=-9.940e-01;MQ_DP=83;QUALapprox=1369;RAW_GT_COUNT=0,1,0;RAW_MQ=291487.00;RAW_MQandDP=291487,83;ReadPosRankSum=-1.480e-01;SB_TABLE=15,26,11,31;VarDP=83
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf.idx
new file mode 100644
index 00000000000..189ac9dc109
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf.idx differ