diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java
index 660bf634393..b40d2620cba 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java
@@ -287,18 +287,15 @@ else if ( clazz.equals(int[].class) ) {
      *
      * @param vc target variant context.
      * @param numAltAllelesToKeep number of alt alleles to keep.
+     * @param ensureReturnContainsAlt make sure the alleles returned include an alternate, even if it's not in the most likely genotype
      * @return the list of alleles to keep, including the reference and {@link Allele#NON_REF_ALLELE} if present
      *
      */
     public static List<Allele> calculateMostLikelyAlleles(final VariantContext vc, final int defaultPloidy,
-                                                          final int numAltAllelesToKeep) {
+                                                          final int numAltAllelesToKeep, boolean ensureReturnContainsAlt) {
         Utils.nonNull(vc, "vc is null");
         Utils.validateArg(defaultPloidy > 0, () -> "default ploidy must be > 0 but defaultPloidy=" + defaultPloidy);
         Utils.validateArg(numAltAllelesToKeep > 0, () -> "numAltAllelesToKeep must be > 0, but numAltAllelesToKeep=" + numAltAllelesToKeep);
-        //allow PLs or GPs (as for GATK-DRAGEN), but we need some kind of genotype data
-        Utils.validateArg(vc.getGenotypes().stream().anyMatch(g -> g.hasPL() || g.hasExtendedAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY)), () -> "Most likely alleles cannot be calculated without likelihoods");
-        //NOTE: this is used in the reblocking case when we have a hom-ref GT and real ALTs
-        final boolean allHomRefData = vc.getGenotypes().stream().allMatch(g -> g.hasPL() && g.getPL()[0] == 0);  //PL=[0,0,0] is okay, we just don't want confident variants
 
         final boolean hasSymbolicNonRef = vc.hasAllele(Allele.NON_REF_ALLELE);
         final int numberOfAllelesThatArentProperAlts = hasSymbolicNonRef ? 2 : 1; 
@@ -308,11 +305,7 @@ public static List<Allele> calculateMostLikelyAlleles(final VariantContext vc, f
             return vc.getAlleles();
         }
 
-        final double[] likelihoodSums = calculateLikelihoodSums(vc, defaultPloidy, allHomRefData);
-        if (MathUtils.sum(likelihoodSums) == 0.0 && !allHomRefData) {
-            throw new IllegalStateException("No likelihood sum exceeded zero -- method was called for variant data " +
-                    "with no variant information.");
-        }
+        final double[] likelihoodSums = calculateLikelihoodSums(vc, defaultPloidy, ensureReturnContainsAlt);
         return filterToMaxNumberOfAltAllelesBasedOnScores(numAltAllelesToKeep, vc.getAlleles(), likelihoodSums);
     }
 
@@ -342,9 +335,12 @@ public static List<Allele> filterToMaxNumberOfAltAllelesBasedOnScores(int numAlt
      *
      * Since GLs are log likelihoods, this quantity is thus
      * SUM_{samples whose likeliest genotype contains this alt allele} log(likelihood alt / likelihood hom ref)
+     * @param vc
+     * @param defaultPloidy
+     * @param countAllelesWithoutHomRef true if we know the input is hom-ref, but we still want to know the most likely ALT
      */
     @VisibleForTesting
-    static double[] calculateLikelihoodSums(final VariantContext vc, final int defaultPloidy, final boolean allHomRefData) {
+    static double[] calculateLikelihoodSums(final VariantContext vc, final int defaultPloidy, final boolean countAllelesWithoutHomRef) {
         final double[] likelihoodSums = new double[vc.getNAlleles()];
         for ( final Genotype genotype : vc.getGenotypes().iterateInSampleNameOrder() ) {
             final GenotypeLikelihoods gls = genotype.getLikelihoods();
@@ -352,7 +348,7 @@ static double[] calculateLikelihoodSums(final VariantContext vc, final int defau
                 continue;
             }
             final double[] glsVector = gls.getAsVector();
-            final int indexOfMostLikelyVariantGenotype = MathUtils.maxElementIndex(glsVector, allHomRefData ? 1 : 0, glsVector.length);
+            final int indexOfMostLikelyVariantGenotype = MathUtils.maxElementIndex(glsVector, countAllelesWithoutHomRef ? 1 : 0, glsVector.length);
             final double GLDiffBetweenRefAndBestVariantGenotype = Math.abs(glsVector[indexOfMostLikelyVariantGenotype] - glsVector[PL_INDEX_OF_HOM_REF]);
             final int ploidy = genotype.getPloidy() > 0 ? genotype.getPloidy() : defaultPloidy;
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
index bb184d693d3..bfc29e9aed7 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
@@ -134,7 +134,7 @@ public VariantContext calculateGenotypes(final VariantContext vc, final Genotype
 
         VariantContext reducedVC = vc;
         if (maxAltAlleles < vc.getAlternateAlleles().size()) {
-            final List<Allele> allelesToKeep = AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, defaultPloidy, maxAltAlleles);
+            final List<Allele> allelesToKeep = AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, defaultPloidy, maxAltAlleles, false);
             final GenotypesContext reducedGenotypes = allelesToKeep.size() == 1 ? GATKVariantContextUtils.subsetToRefOnly(vc, defaultPloidy) :
                     AlleleSubsettingUtils.subsetAlleles(vc.getGenotypes(), defaultPloidy, vc.getAlleles(), allelesToKeep, gpc,
                             GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL);  //with no PLs in some reblocked GVCFs, no-calls are just going to cause problems, so keep 0/0 genotypes as such without trying to recall
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
index d02d60f3618..acb953d3210 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
@@ -505,7 +505,8 @@ protected GenotypeBuilder changeCallToHomRefVersusNonRef(final VariantContext lo
             if (posteriorsKey != null && genotype.hasExtendedAttribute(posteriorsKey)) {
                 subsetHomRefPosteriorsToRefVersusNonRef(lowQualVariant, gb);
             } else {
-                final List<Allele> bestAlleles = AlleleSubsettingUtils.calculateMostLikelyAlleles(lowQualVariant, genotype.getPloidy(), 1);
+                //find best ALT so we can use its likelihood for NON_REF
+                final List<Allele> bestAlleles = AlleleSubsettingUtils.calculateMostLikelyAlleles(lowQualVariant, genotype.getPloidy(), 1, true);
                 final Allele bestAlt = bestAlleles.stream().filter(a -> !a.isReference()).findFirst().orElse(Allele.NON_REF_ALLELE);  //allow span dels
                 //we care about the best alt even though it's getting removed because NON_REF should get the best likelihoods
                 //it shouldn't matter that we're passing in different alt alleles since the GenotypesContext only knows
@@ -928,7 +929,7 @@ private static int[] getGenotypePosteriorsOtherwiseLikelihoods(final Genotype ge
     private void subsetHomRefPosteriorsToRefVersusNonRef(final VariantContext result, final GenotypeBuilder gb) {
         //TODO: bestAlleles needs to be modified for posteriors
         final Genotype genotype = result.getGenotype(0);
-        final List<Allele> bestAlleles = AlleleSubsettingUtils.calculateMostLikelyAlleles(result, genotype.getPloidy(), 1);
+        final List<Allele> bestAlleles = AlleleSubsettingUtils.calculateMostLikelyAlleles(result, genotype.getPloidy(), 1, false);
         final Allele bestAlt = bestAlleles.stream().filter(a -> !a.isReference()).findFirst().orElse(Allele.NON_REF_ALLELE);  //allow span dels
         final int[] idxVector = result.getGLIndicesOfAlternateAllele(bestAlt);
         final int[] multiallelicPLs = getGenotypePosteriorsOtherwiseLikelihoods(genotype, posteriorsKey);
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
index c52e2c7aab5..f56ff949e47 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
@@ -159,6 +159,7 @@ public Object[][] gvcfsToGenotype() {
                         b37_reference_20_21},
 
                 //23 highly multi-allelic sites across 54 1000G exomes to test allele subsetting and QUAL calculation
+                //plus one 10-allele WGS variant that's all hom-ref with one GT that has unnormalized PLs from some sort of GenomicsDB corner case
                 {getTestFile("multiallelicQualRegression.vcf "),
                         getTestFile("multiallelicQualRegression.expected.vcf"),
                         NO_EXTRA_ARGS, hg38Reference}
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtilsUnitTest.java
index a5061033f6d..ab26f27869b 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtilsUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtilsUnitTest.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.hellbender.tools.walkers.genotyper;
 
 import htsjdk.variant.variantcontext.*;
-import htsjdk.variant.vcf.VCFConstants;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.MathUtils;
 import org.broadinstitute.hellbender.GATKBaseTest;
@@ -288,7 +287,7 @@ public Object[][] makeUpdatePLsSACsAndADData() {
     public void testCalculateMostLikelyAllelesTieDoesntRemoveAllTiedAlleles(){
         VariantContext vc = new VariantContextBuilder(null, "1", 100, 100, Arrays.asList(Aref, C, G))
                 .genotypes(Arrays.asList(new GenotypeBuilder("sample1", Arrays.asList(C,G)).PL( new double[]{5, 5, 5, 5, 0, 5}).make())).make();
-        Assert.assertEquals(AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, 2, 1), Arrays.asList(Aref,C)) ;
+        Assert.assertEquals(AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, 2, 1, false), Arrays.asList(Aref,C)) ;
     }
 
     @DataProvider
@@ -315,9 +314,9 @@ public void testThatFilteringWorksCorrectly(int numToKeep, List<Allele> alleles,
     @Test
     public void testCalculateMostLikelyAllelesPreconditions(){
         VariantContext vc = new VariantContextBuilder(null, "1", 100, 100, Arrays.asList(Aref, C, G)).make();
-        Assert.assertThrows(IllegalArgumentException.class, () -> AlleleSubsettingUtils.calculateMostLikelyAlleles(null, 2, 2));
-        Assert.assertThrows(IllegalArgumentException.class, () -> AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, 0, 2));
-        Assert.assertThrows(IllegalArgumentException.class, () -> AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, 2, 0));
+        Assert.assertThrows(IllegalArgumentException.class, () -> AlleleSubsettingUtils.calculateMostLikelyAlleles(null, 2, 2, false));
+        Assert.assertThrows(IllegalArgumentException.class, () -> AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, 0, 2, false));
+        Assert.assertThrows(IllegalArgumentException.class, () -> AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, 2, 0, false));
     }
 
     @Test
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 4f8175e6748..8d75c7d5c16 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -1404,7 +1404,7 @@ public void testMaxAlternateAlleles(final String bam, final String reference, fi
         final Map<SimpleInterval, List<Allele>> expectedSubsettedAllelesByLocus = new HashMap<>();
         for ( final VariantContext vc : callsNoMaxAlternateAlleles ) {
             if ( getNumAltAllelesExcludingNonRef(vc) > maxAlternateAlleles ) {
-                final List<Allele> mostLikelyAlleles = AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, HomoSapiensConstants.DEFAULT_PLOIDY, maxAlternateAlleles);
+                final List<Allele> mostLikelyAlleles = AlleleSubsettingUtils.calculateMostLikelyAlleles(vc, HomoSapiensConstants.DEFAULT_PLOIDY, maxAlternateAlleles, false);
                 expectedSubsettedAllelesByLocus.put(new SimpleInterval(vc), mostLikelyAlleles);
             }
         }
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.vcf
index 319814ca3e3..79b4848bd53 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.vcf
@@ -55,3375 +55,12 @@
 ##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">
 ##contig=<ID=chr1,length=248956422,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr2,length=242193529,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr3,length=198295559,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr4,length=190214555,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr5,length=181538259,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr6,length=170805979,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr7,length=159345973,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr8,length=145138636,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr9,length=138394717,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr10,length=133797422,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr11,length=135086622,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr12,length=133275309,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr13,length=114364328,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14,length=107043718,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr15,length=101991189,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr16,length=90338345,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr17,length=83257441,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr18,length=80373285,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr19,length=58617616,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr20,length=64444167,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr21,length=46709983,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr22,length=50818468,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrX,length=156040895,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrY,length=57227415,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrM,length=16569,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270706v1_random,length=175055,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270707v1_random,length=32032,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270708v1_random,length=127682,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270709v1_random,length=66860,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270710v1_random,length=40176,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270711v1_random,length=42210,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270712v1_random,length=176043,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270713v1_random,length=40745,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr1_KI270714v1_random,length=41717,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr2_KI270715v1_random,length=161471,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr2_KI270716v1_random,length=153799,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr3_GL000221v1_random,length=155397,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr4_GL000008v2_random,length=209709,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr5_GL000208v1_random,length=92689,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr9_KI270717v1_random,length=40062,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr9_KI270718v1_random,length=38054,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr9_KI270719v1_random,length=176845,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr9_KI270720v1_random,length=39050,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr11_KI270721v1_random,length=100316,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14_GL000009v2_random,length=201709,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14_GL000225v1_random,length=211173,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14_KI270722v1_random,length=194050,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14_GL000194v1_random,length=191469,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14_KI270723v1_random,length=38115,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14_KI270724v1_random,length=39555,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14_KI270725v1_random,length=172810,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr14_KI270726v1_random,length=43739,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr15_KI270727v1_random,length=448248,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr16_KI270728v1_random,length=1872759,assembly=Homo_sapiens_assembly38.fasta.gz>
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-##contig=<ID=chr22_KI270734v1_random,length=165050,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr22_KI270735v1_random,length=42811,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr22_KI270736v1_random,length=181920,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr22_KI270737v1_random,length=103838,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr22_KI270738v1_random,length=99375,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chr22_KI270739v1_random,length=73985,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrY_KI270740v1_random,length=37240,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270302v1,length=2274,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270304v1,length=2165,assembly=Homo_sapiens_assembly38.fasta.gz>
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-##contig=<ID=chrUn_KI270305v1,length=1472,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270322v1,length=21476,assembly=Homo_sapiens_assembly38.fasta.gz>
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-##contig=<ID=chrUn_KI270310v1,length=1201,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270316v1,length=1444,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270315v1,length=2276,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270312v1,length=998,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270311v1,length=12399,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270317v1,length=37690,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270412v1,length=1179,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270411v1,length=2646,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270414v1,length=2489,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270419v1,length=1029,assembly=Homo_sapiens_assembly38.fasta.gz>
-##contig=<ID=chrUn_KI270418v1,length=2145,assembly=Homo_sapiens_assembly38.fasta.gz>
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 ##source=GenomicsDBImport
 ##source=SelectVariants
+##note="first variant from warp WGS test, rest from warp 1KG WEx JG test"
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CHMI_CHMI3_Nex1	NA12878	NA12891	NA12892	NA19238	NA20845	NA20846	NA20847	NA20849	NA20850	NA20851	NA20852	NA20853	NA20854	NA20856	NA20858	NA20859	NA20861	NA20862	NA20866	NA20869	NA20870	NA20871	NA20872	NA20873	NA20874	NA20875	NA20876	NA20877	NA20878	NA20881	NA20885	NA20886	NA20887	NA20888	NA20889	NA20890	NA20891	NA20892	NA20893	NA20894	NA20895	NA20896	NA20897	NA20898	NA20899	NA20901	NA20902	NA20903	NA20904	NA20905	NA20906	NA20908	NA20910	NA20911	NA21086	NA21087	NA21088	NA21093	NA21095	NA21114	NA21124	NA21126	NA21129	NA21137
+chr1	931135	.	TCCC	TGCCC,ACCC,TACCC,TACCCC,T,GCCC,CCCC,TCCCCGGGGCCC,*,<NON_REF>	.	.	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 chr1	3836468	.	GTTTT	GTTTTT,GTTTTTTT,G,GTTT,GTT,GT,GTTTTTT,<NON_REF>	.	.	AS_QUALapprox=|286|166|103|29|87|28|403|0;AS_RAW_BaseQRankSum=|-0.700,1|0.000,1,1.300,1|-0.800,1|-2.300,1|0.000,1,0.600,1|0.800,1|0.600,1,1.000,1|;AS_RAW_MQ=172286.000|86400.000|24825.000|14400.000|21600.000|14400.000|14400.000|49587.000|0.000;AS_RAW_MQRankSum=|0.000,1|-1.100,1,-0.700,1|1.100,1|1.200,1|1.500,1,1.600,1|0.000,1|-0.900,1,-0.800,1|;AS_RAW_ReadPosRankSum=|0.300,1|-2.700,1,0.600,1|-1.000,1|-1.000,1|-0.600,1,-0.200,1|0.500,1|-0.800,1,-0.300,1|;AS_SB_TABLE=53,5|20,2|9,0|3,1|4,2|4,0|3,1|20,1|0,0;AS_VarDP=58|24|9|4|6|4|4|21|0;BaseQRankSum=0;DP=2100;MQRankSum=0;QUALapprox=1141;RAW_GT_COUNT=0,8,3;RAW_MQandDP=1647249,550;ReadPosRankSum=-0.23;VarDP=145	GT:AD:GQ:PL:SB:DP	0/1:11,22,0,0,0,0,0,0,0:99:239,0,174,338,219,636,338,219,636,636,338,219,636,636,636,338,219,636,636,636,636,338,219,636,636,636,636,636,338,219,636,636,636,636,636,636,338,219,636,636,636,636,636,636,636:11,0,29,4:44	0/0:.:50:.:.:27	0/0:.:10:.:.:30	0/0:.:10:.:.:28	0/0:.:0:.:.:3	0/0:.:60:.:.:27	0/0:.:30:.:.:59	0/2:3,0,7,0,0,0,0,0,0:59:132,142,223,0,80,59,142,223,80,223,142,223,80,223,223,142,223,80,223,223,223,142,223,80,223,223,223,223,142,223,80,223,223,223,223,223,142,223,80,223,223,223,223,223,223:3,0,7,0:10	0/0:.:60:.:.:33	0/0:.:60:.:.:31	.:.:.:.:.:.	0/0:.:60:.:.:27	0/0:.:60:.:.:30	0/0:.:40:.:.:51	0/0:.:60:.:.:29	0/0:.:60:.:.:31	0/3:8,0,0,4,0,0,0,0,0:99:103,160,534,160,534,534,0,437,437,670,160,534,534,437,534,160,534,534,437,534,534,160,534,534,437,534,534,534,160,534,534,437,534,534,534,534,160,534,534,437,534,534,534,534,534:8,0,5,1:14	0/0:.:60:.:.:30	0/0:.:60:.:.:32	0/0:.:60:.:.:37	0/0:.:40:.:.:49	0/0:.:60:.:.:36	0/2:2,0,2,0,0,0,0,0,0:34:34,42,113,0,71,65,42,113,71,113,42,113,71,113,113,42,113,71,113,113,113,42,113,71,113,113,113,113,42,113,71,113,113,113,113,113,42,113,71,113,113,113,113,113,113:0,2,2,0:4	0/4:10,0,0,0,4,0,0,0,0:19:19,48,195,48,195,195,48,195,195,195,0,147,147,147,135,48,195,195,195,147,195,48,195,195,195,147,195,195,48,195,195,195,147,195,195,195,48,195,195,195,147,195,195,195,195:9,1,2,2:14	0/0:.:30:.:.:58	0/0:.:60:.:.:32	0/5:11,0,0,0,0,2,0,0,0:20:20,54,305,54,305,305,54,305,305,305,54,305,305,305,305,0,251,251,251,251,245,54,305,305,305,305,251,305,54,305,305,305,305,251,305,305,54,305,305,305,305,251,305,305,305:11,0,2,0:13	0/0:.:60:.:.:26	0/0:.:60:.:.:26	0/0:.:60:.:.:32	.:.:.:.:.:.	0/0:.:60:.:.:29	6/7:1,0,0,0,0,0,4,6,0:47:141,222,534,222,534,534,222,534,534,534,222,534,534,534,534,222,534,534,534,534,534,113,472,472,472,472,472,742,47,137,137,137,137,137,0,82,222,534,534,534,534,534,472,137,534:0,1,9,1:11	0/0:.:10:.:.:40	0/0:.:60:.:.:41	0/0:.:60:.:.:30	0/7:2,0,0,0,0,0,0,9,0:10:186,193,234,193,234,234,193,234,234,234,193,234,234,234,234,193,234,234,234,234,234,193,234,234,234,234,234,234,0,41,41,41,41,41,41,10,193,234,234,234,234,234,234,41,234:1,1,8,1:11	0/0:.:20:.:.:43	4/7:0,0,0,0,2,0,0,6,0:30:153,176,228,176,228,228,176,228,228,228,143,196,196,196,229,176,228,228,228,196,228,176,228,228,228,196,228,228,30,54,54,54,0,54,54,41,176,228,228,228,196,228,228,54,228:0,0,8,0:8	0/0:.:10:.:.:28	0/0:.:60:.:.:29	.:.:.:.:.:.	0/0:.:60:.:.:30	0/5:10,0,0,0,0,2,0,0,0:67:67,155,689,155,689,689,155,689,689,689,155,689,689,689,689,0,279,279,279,279,163,155,689,689,689,689,279,689,155,689,689,689,689,279,689,689,155,689,689,689,689,279,689,689,689:10,0,3,1:14	0/0:.:30:.:.:34	0/0:.:50:.:.:23	0/0:.:50:.:.:37	0/0:.:60:.:.:29	0/0:.:30:.:.:34	0/0:.:20:.:.:43	.:.:.:.:.:.	0/0:.:60:.:.:31	0/0:.:60:.:.:39	0/0:.:60:.:.:28	0/0:.:60:.:.:36	0/0:.:60:.:.:38	0/0:.:30:.:.:36	0/0:.:50:.:.:31	0/0:.:50:.:.:29	.:.:.:.:.:.	0/0:.:60:.:.:33	.:.:.:.:.:.	1/1:0,2,0,0,0,0,0,0,0:8:47,8,0,47,8,47,47,8,47,47,47,8,47,47,47,47,8,47,47,47,47,47,8,47,47,47,47,47,47,8,47,47,47,47,47,47,47,8,47,47,47,47,47,47,47:0,0,2,0:2	0/0:.:10:.:.:15	.:.:.:.:.:.
 chr1	11055120	.	CTTT	CTTTT,C,CT,CTT,CTTTTT,CTTTTTT,CTTTTTTT,<NON_REF>	.	.	AS_QUALapprox=|849|188|791|2396|782|210|124|52;AS_RAW_BaseQRankSum=|-1.400,1,-0.800,1,-0.700,1,-0.600,2,-0.300,1,-0.100,1,0.300,1,0.500,1,1.300,1,1.700,1|0.300,1,0.700,1|-0.900,2,0.400,1,0.600,1,1.200,1,1.500,1,1.700,1|-1.700,1,-1.200,1,-0.900,2,-0.600,1,-0.500,1,-0.300,1,-0.100,1,0.000,4,0.100,2,0.200,1,0.300,1,0.400,3,0.600,1,0.900,1,1.000,1,1.300,1,1.500,1|-0.700,1,-0.500,1,0.000,1,0.200,1,0.500,1,1.100,1,2.100,1|0.700,1|0.900,1|;AS_RAW_MQ=1085181.000|189482.000|14400.000|118449.000|571392.000|105461.000|14400.000|12164.000|0.000;AS_RAW_MQRankSum=|-1.400,1,-0.700,3,-0.300,2,0.000,2,0.200,2,0.800,1|0.000,1,0.700,1|0.000,5,1.200,1,1.300,1|-1.400,1,-1.000,1,-0.900,2,-0.800,1,-0.600,1,-0.400,2,-0.200,1,0.000,4,0.100,1,0.400,1,0.600,2,0.700,1,0.900,2,1.000,1,1.100,1,1.600,1,1.700,1|-1.400,2,-1.200,1,-0.500,1,0.000,2,0.600,1|0.000,1|-1.500,1|;AS_RAW_ReadPosRankSum=|-2.200,1,-0.800,1,-0.600,2,-0.400,1,0.100,1,0.200,1,0.400,1,1.000,1,1.200,1,1.500,1|0.900,1,1.300,1|-1.100,1,-0.800,1,-0.500,1,-0.200,1,-0.100,1,0.000,1,1.000,1|-2.400,1,-2.000,1,-1.300,1,-1.200,1,-1.100,1,-1.000,2,-0.700,1,-0.500,1,-0.400,1,-0.100,1,0.000,1,0.200,1,0.300,1,0.600,2,0.800,1,1.000,1,1.400,1,1.600,1,1.900,1,2.100,2,2.800,1|-2.100,1,-0.900,1,-0.500,1,-0.400,1,-0.300,1,-0.100,1,0.600,1|2.200,1|0.400,1|;AS_SB_TABLE=18,301|3,56|1,3|1,32|1,164|4,29|2,2|0,4|0,0;AS_VarDP=319|59|4|33|165|33|4|4|0;BaseQRankSum=0.238;DP=2097;MQRankSum=0;QUALapprox=4814;RAW_GT_COUNT=0,35,9;RAW_MQandDP=6194030,1778;ReadPosRankSum=0.085;VarDP=704	GT:AD:GQ:PL:SB:DP	0/1:10,10,0,0,0,0,0,0,0:99:101,0,197,162,214,410,162,214,410,410,162,214,410,410,410,162,214,410,410,410,410,162,214,410,410,410,410,410,162,214,410,410,410,410,410,410,162,214,410,410,410,410,410,410,410:0,10,1,14:25	.:.:.:.:.:.	.:.:.:.:.:.	.:.:.:.:.:.	0/2:6,0,2,0,0,0,0,0,0:66:66,84,235,0,151,144,84,235,151,235,84,235,151,235,235,84,235,151,235,235,235,84,235,151,235,235,235,235,84,235,151,235,235,235,235,235,84,235,151,235,235,235,235,235,235:4,2,1,1:8	0/3:14,0,0,7,0,0,0,0,0:99:213,196,598,196,598,598,0,425,425,396,196,598,598,425,598,196,598,598,425,598,598,196,598,598,425,598,598,598,196,598,598,425,598,598,598,598,196,598,598,425,598,598,598,598,598:2,12,0,15:29	0/4:11,0,0,0,13,0,0,0,0:99:190,222,421,222,421,421,222,421,421,421,0,199,199,199,161,222,421,421,421,199,421,222,421,421,421,199,421,421,222,421,421,421,199,421,421,421,222,421,421,421,199,421,421,421,421:0,11,0,13:24	0/3:17,0,0,3,0,0,0,0,0:40:40,91,501,91,501,501,0,410,410,400,91,501,501,410,501,91,501,501,410,501,501,91,501,501,410,501,501,501,91,501,501,410,501,501,501,501,91,501,501,410,501,501,501,501,501:0,17,0,3:20	.:.:.:.:.:.	.:.:.:.:.:.	0/3:8,0,0,7,0,0,0,0,0:99:152,218,553,218,553,553,0,328,328,375,218,553,553,328,553,218,553,553,328,553,553,218,553,553,328,553,553,553,218,553,553,328,553,553,553,553,218,553,553,328,553,553,553,553,553:0,8,2,12:22	0/4:16,0,0,0,5,0,0,0,0:75:75,125,440,125,440,440,125,440,440,440,0,245,245,245,184,125,440,440,440,245,440,125,440,440,440,245,440,440,125,440,440,440,245,440,440,440,125,440,440,440,245,440,440,440,440:1,15,0,8:24	0/5:5,0,0,0,0,4,0,0,0:66:66,116,328,116,328,328,116,328,328,328,116,328,328,328,328,0,202,202,202,202,243,116,328,328,328,328,202,328,116,328,328,328,328,202,328,328,116,328,328,328,328,202,328,328,328:0,5,1,9:15	4/5:3,0,0,0,6,6,0,0,0:68:174,215,360,215,360,360,215,360,360,360,83,186,186,186,191,68,207,207,207,0,239,215,360,360,360,186,207,360,215,360,360,360,186,207,360,360,215,360,360,360,186,207,360,360,360:0,3,0,12:15	0/4:3,0,0,0,3,0,0,0,0:59:59,76,167,76,167,167,76,167,167,167,0,90,90,90,76,76,167,167,167,90,167,76,167,167,167,90,167,167,76,167,167,167,90,167,167,167,76,167,167,167,90,167,167,167,167:0,3,0,7:10	4/1:2,6,0,0,9,0,0,0,0:95:225,150,236,273,233,391,273,233,391,391,95,0,199,199,229,273,233,391,391,199,391,273,233,391,391,199,391,391,273,233,391,391,199,391,391,391,273,233,391,391,199,391,391,391,391:0,2,0,15:17	0/5:5,0,0,0,0,3,0,0,0:75:75,98,215,98,215,215,98,215,215,215,98,215,215,215,215,0,136,136,136,136,180,98,215,215,215,215,136,215,98,215,215,215,215,136,215,215,98,215,215,215,215,136,215,215,215:0,5,0,8:13	3/5:5,0,0,6,0,9,0,0,0:39:197,261,530,261,530,530,74,336,336,400,261,530,530,336,530,39,241,241,0,241,244,261,530,530,336,530,241,530,261,530,530,336,530,241,530,530,261,530,530,336,530,241,530,530,530:0,5,2,13:20	0/3:8,0,0,5,0,0,0,0,0:99:128,135,300,135,300,300,0,196,196,225,135,300,300,196,300,135,300,300,196,300,300,135,300,300,196,300,300,300,135,300,300,196,300,300,300,300,135,300,300,196,300,300,300,300,300:0,8,0,8:16	4/1:1,4,0,0,9,0,0,0,0:50:246,225,338,264,250,333,264,250,333,333,50,0,118,118,77,264,250,333,333,118,333,264,250,333,333,118,333,333,264,250,333,333,118,333,333,333,264,250,333,333,118,333,333,333,333:0,1,0,18:19	0/4:8,0,0,0,5,0,0,0,0:63:63,166,639,166,639,639,166,639,639,639,0,222,222,222,170,166,639,639,639,222,639,166,639,639,639,222,639,639,166,639,639,639,222,639,639,639,166,639,639,639,222,639,639,639,639:0,8,0,7:15	4/1:4,5,0,0,8,0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 chr1	11080563	.	AACACAC	AACACACAC,AACAC,A,AAC,CACACAC,AACACACACAC,ACACACAC,AAACACACAC,<NON_REF>	.	.	AS_QUALapprox=|830|949|6317|1836|1976|978|1304|736|724;AS_RAW_BaseQRankSum=|-2.600,1,-0.400,1,0.000,1,0.200,1,0.600,2|-0.600,1,0.000,2,0.200,1,0.600,1,0.900,1|-0.400,1,-0.300,2,-0.200,1,0.100,1,0.400,1,0.600,2,0.700,1,0.900,1,1.000,1,1.800,1|0.000,1,0.200,1,0.600,2,0.900,2|0.000,1,0.200,1,0.600,3,0.900,1|0.000,1,0.200,1,0.600,2,0.900,1|0.000,1,0.200,1,0.600,2,0.900,1|0.000,1,0.200,1,0.600,2,0.900,1|0.000,1,0.200,1,0.600,2,0.900,1;AS_RAW_MQ=879551.000|13361.000|21200.000|350230.000|87817.000|17789.000|8800.000|0.000|0.000|90052.000;AS_RAW_MQRankSum=|-3.300,1,-1.300,1,-0.300,1,0.000,1,0.300,1,1.300,1|-1.300,1,-1.100,1,-0.400,1,-0.300,1,0.100,1,1.300,1|-3.200,1,-1.600,1,-1.100,1,-0.400,2,-0.300,1,-0.200,1,0.200,1,0.300,2,0.800,1,0.900,1|-3.500,1,-1.300,1,-1.100,1,-0.300,1,0.300,1,1.300,1|-1.300,1,-1.100,1,-0.300,1,0.000,1,0.300,1,1.300,1|-1.300,1,-1.100,1,-0.300,1,0.300,1,1.300,1|-1.300,1,-1.100,1,-0.300,1,0.300,1,1.300,1|-1.300,1,-1.100,1,-0.300,1,0.300,1,1.300,1|-1.300,1,-1.100,1,-0.300,1,0.300,1,1.300,1;AS_RAW_ReadPosRankSum=|-1.700,1,-1.400,1,0.300,1,0.600,2,1.900,1|-1.400,1,-0.600,1,0.300,2,0.600,1,1.200,1|-1.800,1,-1.700,1,-1.500,1,-0.600,1,-0.400,2,0.400,1,0.600,2,1.000,1,1.500,1,2.200,1|-1.700,1,-1.400,1,-0.600,1,-0.500,1,0.300,1,0.600,1|-1.700,1,-1.400,1,-0.600,1,0.300,1,0.600,1,1.400,1|-1.700,1,-1.400,1,-0.600,1,0.300,1,0.600,1|-1.700,1,-1.400,1,-0.600,1,0.300,1,0.600,1|-1.700,1,-1.400,1,-0.600,1,0.300,1,0.600,1|-1.700,1,-1.400,1,-0.600,1,0.300,1,0.600,1;AS_SB_TABLE=47,212|3,2|1,6|13,103|5,21|2,4|0,3|0,0|0,0|5,22;AS_VarDP=256|11|10|143|26|3|5|1|0|0;BaseQRankSum=0.475;DP=3280;MQRankSum=-0.22;QUALapprox=9035;RAW_GT_COUNT=0,14,10;RAW_MQandDP=4464534,1328;ReadPosRankSum=0.644;VarDP=533	GT:AD:GQ:PL:SB:DP	0/1:26,9,0,0,0,0,0,0,0,0:36:36,0,1006,236,1081,1900,236,1081,1900,1900,236,1081,1900,1900,1900,236,1081,1900,1900,1900,1900,236,1081,1900,1900,1900,1900,1900,236,1081,1900,1900,1900,1900,1900,1900,236,1081,1900,1900,1900,1900,1900,1900,1900,236,1081,1900,1900,1900,1900,1900,1900,1900,1900:4,6,17,7:51	0/0:.:10:.:.:26	0/0:.:20:.:.:31	0/0:.:0:.:.:26	0/0:.:10:.:.:7	0/2:9,0,3,0,0,0,0,0,0,0:9:9,96,1297,0,1147,1124,96,1297,1147,1297,96,1297,1147,1297,1297,96,1297,1147,1297,1297,1297,96,1297,1147,1297,1297,1297,1297,96,1297,1147,1297,1297,1297,1297,1297,96,1297,1147,1297,1297,1297,1297,1297,1297,96,1297,1147,1297,1297,1297,1297,1297,1297,1297:1,8,0,4:13	0/0:.:60:.:.:69	3/4:0,0,0,7,11,0,0,0,0,0:99:676,559,526,559,526,526,254,258,258,220,156,154,154,0,103,559,526,526,258,154,526,559,526,526,258,154,526,526,559,526,526,258,154,526,526,526,559,526,526,258,154,526,526,526,526,559,526,526,258,154,526,526,526,526,526:0,0,4,14:18	0/3:7,0,0,9,0,0,0,0,0,0:99:575,480,731,480,731,731,0,301,301,465,480,731,731,301,731,480,731,731,301,731,731,480,731,731,301,731,731,731,480,731,731,301,731,731,731,731,480,731,731,301,731,731,731,731,731,480,731,731,301,731,731,731,731,731,731:2,5,0,11:18	3/4:0,0,0,7,5,0,0,0,0,0:91:584,462,445,462,445,445,169,171,171,193,124,137,137,0,91,462,445,445,171,137,445,462,445,445,171,137,445,445,462,445,445,171,137,445,445,445,462,445,445,171,137,445,445,445,445,462,445,445,171,137,445,445,445,445,445:0,0,3,11:14	0/0:.:60:.:.:67	0/3:7,0,0,2,0,0,0,0,0,0:99:220,146,534,146,534,534,0,389,389,364,146,534,534,389,534,146,534,534,389,534,534,146,534,534,389,534,534,534,146,534,534,389,534,534,534,534,146,534,534,389,534,534,534,534,534,146,534,534,389,534,534,534,534,534,534:0,7,0,3:10	0/0:.:20:.:.:21	0/0:.:0:.:.:25	0/0:.:30:.:.:35	5/6:0,0,0,0,0,3,5,0,0,0:99:1113,1143,1292,1143,1292,1292,1143,1292,1292,1292,1143,1292,1292,1292,1292,177,332,332,332,332,897,859,911,911,911,911,0,874,1143,1292,1292,1292,1292,332,911,1292,1143,1292,1292,1292,1292,332,911,1292,1292,1143,1292,1292,1292,1292,332,911,1292,1292,1292:0,0,2,16:18	0/0:.:50:.:.:14	3/3:1,0,0,17,0,0,0,0,0,0:37:736,739,757,739,757,757,37,55,55,0,739,757,757,55,757,739,757,757,55,757,757,739,757,757,55,757,757,757,739,757,757,55,757,757,757,757,739,757,757,55,757,757,757,757,757,739,757,757,55,757,757,757,757,757,757:0,1,2,15:18	0/1:29,2,0,0,0,0,0,0,0,0:70:70,0,1160,160,1180,1440,160,1180,1440,1440,160,1180,1440,1440,1440,160,1180,1440,1440,1440,1440,160,1180,1440,1440,1440,1440,1440,160,1180,1440,1440,1440,1440,1440,1440,160,1180,1440,1440,1440,1440,1440,1440,1440,160,1180,1440,1440,1440,1440,1440,1440,1440,1440:7,22,0,2:31	0/0:.:60:.:.:61	0/0:.:60:.:.:61	0/0:.:60:.:.:72	0/3:12,0,0,7,0,0,0,0,0,0:99:238,274,759,274,759,759,0,486,486,462,274,759,759,486,759,274,759,759,486,759,759,274,759,759,486,759,759,759,274,759,759,486,759,759,759,759,274,759,759,486,759,759,759,759,759,274,759,759,486,759,759,759,759,759,759:2,10,1,6:19	0/0:.:50:.:.:65	0/0:.:50:.:.:59	0/0:.:40:.:.:49	0/0:.:60:.:.:62	0/5:11,0,0,0,0,1,0,0,0,0:71:71,202,1661,202,1661,1661,202,1661,1661,1661,202,1661,1661,1661,1661,0,587,587,587,587,745,202,1661,1661,1661,1661,587,1661,202,1661,1661,1661,1661,587,1661,1661,202,1661,1661,1661,1661,587,1661,1661,1661,202,1661,1661,1661,1661,587,1661,1661,166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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.vcf.idx
index 90f10b9024e..e29984d6567 100644
Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.vcf.idx differ