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 b40d2620cba..9422472b9fe 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
@@ -7,12 +7,14 @@
 import htsjdk.variant.vcf.*;
 import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.exceptions.UserException;
+import org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils;
 import org.broadinstitute.hellbender.utils.genotyper.GenotypePriorCalculator;
 import org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger;
 import org.broadinstitute.hellbender.utils.MathUtils;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.collections.Permutation;
 import org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList;
+import org.broadinstitute.hellbender.utils.logging.OneShotLogger;
 import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.hellbender.utils.variant.VariantContextGetters;
@@ -33,9 +35,18 @@ private AlleleSubsettingUtils() {}  // prevent instantiation
     private static final int PL_INDEX_OF_HOM_REF = 0;
     public static final int NUM_OF_STRANDS = 2; // forward and reverse strands
 
-    private static final GenotypeLikelihoodCalculators GL_CALCS = new GenotypeLikelihoodCalculators();
+    private static final OneShotLogger attributesRemovedOneShotLogger = new OneShotLogger(AlleleSubsettingUtils.class);
 
+    private static final GenotypeLikelihoodCalculators GL_CALCS = new GenotypeLikelihoodCalculators();
 
+    public static GenotypesContext subsetAlleles(final GenotypesContext originalGs, final int defaultPloidy,
+                                                 final List<Allele> originalAlleles,
+                                                 final List<Allele> allelesToKeep,
+                                                 final GenotypePriorCalculator gpc,
+                                                 final GenotypeAssignmentMethod assignmentMethod) {
+        //TODO: if other usages of this method should update or remove A,R, or G length annotations then header parsing is necessary and the method below should be used
+        return subsetAlleles(originalGs, defaultPloidy, originalAlleles, allelesToKeep, gpc, assignmentMethod, Collections.emptyList());
+    }
     /**
      * Create the new GenotypesContext with the subsetted PLs and ADs
      *
@@ -45,13 +56,15 @@ private AlleleSubsettingUtils() {}  // prevent instantiation
      * @param originalAlleles          the original alleles
      * @param allelesToKeep            the subset of alleles to use with the new Genotypes
      * @param assignmentMethod         assignment strategy for the (subsetted) PLs
+     * @param alleleBasedLengthAnnots  list of annotations that have lengths based on the number of alleles (A, R, and G length types)
      * @return                         a new non-null GenotypesContext
      */
     public static GenotypesContext subsetAlleles(final GenotypesContext originalGs, final int defaultPloidy,
                                                  final List<Allele> originalAlleles,
                                                  final List<Allele> allelesToKeep,
                                                  final GenotypePriorCalculator gpc,
-                                                 final GenotypeAssignmentMethod assignmentMethod) {
+                                                 final GenotypeAssignmentMethod assignmentMethod,
+                                                 final List<String> alleleBasedLengthAnnots) {
         Utils.nonNull(originalGs, "original GenotypesContext must not be null");
         Utils.nonNull(allelesToKeep, "allelesToKeep is null");
         Utils.nonEmpty(allelesToKeep, "must keep at least one allele");
@@ -93,9 +106,23 @@ public static GenotypesContext subsetAlleles(final GenotypesContext originalGs,
             final GenotypeBuilder gb = new GenotypeBuilder(g);
             final Map<String, Object> attributes = new HashMap<>(g.getExtendedAttributes());
             attributes.remove(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY);
-            //TODO: remove other G-length attributes, although that may require header parsing
             attributes.remove(VCFConstants.GENOTYPE_POSTERIORS_KEY);
             attributes.remove(GATKVCFConstants.GENOTYPE_PRIOR_KEY);
+            final List<String> attributesToRemove = new ArrayList<>();
+            for(final String attribute : attributes.keySet()) {
+                if (alleleBasedLengthAnnots.contains(attribute)) {
+                    if (attribute.equals(GATKVCFConstants.F1R2_KEY) || attribute.equals(GATKVCFConstants.F2R1_KEY)) {
+                        final String oldAttributeString = (String) attributes.get(attribute);
+                        final String[] oldAttributeArray = oldAttributeString.split(AnnotationUtils.LIST_DELIMITER);
+                        final int[] oldAttribute = Arrays.stream(oldAttributeArray).mapToInt(Integer::parseInt).toArray();
+                        final int[] newAttribute = getNewAlleleBasedReadCountAnnotation(allelesToKeep, allelePermutation, oldAttribute);
+                        attributes.put(attribute, newAttribute);
+                    } else {
+                        attributesToRemove.add(attribute);
+                    }
+                }
+            }
+            attributesToRemove.forEach(attributes::remove);
             gb.noPL().noGQ().noAttributes().attributes(attributes);  //if alleles are subset, old PLs and GQ are invalid
             if (newLog10GQ != Double.NEGATIVE_INFINITY && g.hasGQ()) {  //only put GQ if originally present
                 gb.log10PError(newLog10GQ);
@@ -112,19 +139,39 @@ public static GenotypesContext subsetAlleles(final GenotypesContext originalGs,
 
             // restrict AD to the new allele subset
             if(g.hasAD()) {
-                final int[] oldAD = g.getAD();
-                final int[] newAD = IntStream.range(0, allelesToKeep.size()).map(n -> oldAD[allelePermutation.fromIndex(n)]).toArray();
-                final int nonRefIndex = allelesToKeep.indexOf(Allele.NON_REF_ALLELE);
-                if (nonRefIndex != -1 && nonRefIndex < newAD.length) {
-                    newAD[nonRefIndex] = 0;  //we will "lose" coverage here, but otherwise merging NON_REF AD counts with other alleles "creates" reads
-                }
+                final int[] newAD = getNewAlleleBasedReadCountAnnotation(allelesToKeep, allelePermutation, g.getAD());
                 gb.AD(newAD);
+                // if we have recalculated AD and the original genotype had AF but was then removed, then recalculate AF based on AD counts
+                if (alleleBasedLengthAnnots.contains(GATKVCFConstants.ALLELE_FRACTION_KEY) && g.hasExtendedAttribute(GATKVCFConstants.ALLELE_FRACTION_KEY)) {
+                    attributesToRemove.remove(GATKVCFConstants.ALLELE_FRACTION_KEY);
+                    final double[] newAFs = MathUtils.normalizeSumToOne(Arrays.stream(newAD).mapToDouble(x -> x).toArray());
+                    gb.attribute(GATKVCFConstants.ALLELE_FRACTION_KEY, Arrays.copyOfRange(newAFs, 1, newAFs.length)); //omit the first entry of the array corresponding to the reference
+                }
+            }
+            if (attributesToRemove.size() > 0) {
+                attributesRemovedOneShotLogger.warn(() -> "The following attributes have been removed at sites where alleles were subset: " + String.join(",", attributesToRemove));
             }
             newGTs.add(gb.make());
         }
         return newGTs;
     }
 
+    /**
+     * Subsets allele length annotation to match the alleles that have been kept
+     * @param allelesToKeep     list of alleles that are not being filtered out
+     * @param allelePermutation permutation that matches the index from the old annotation to the new annotation given which alleles have been removed
+     * @param oldAnnot          the original annotation
+     * @return                  the new subset annotation
+     */
+    private static int[] getNewAlleleBasedReadCountAnnotation(List<Allele> allelesToKeep, Permutation<Allele> allelePermutation, int[] oldAnnot) {
+        final int[] newAnnot = IntStream.range(0, allelesToKeep.size()).map(n -> oldAnnot[allelePermutation.fromIndex(n)]).toArray();
+        final int nonRefIndex = allelesToKeep.indexOf(Allele.NON_REF_ALLELE);
+        if (nonRefIndex != -1 && nonRefIndex < newAnnot.length) {
+            newAnnot[nonRefIndex] = 0;  //we will "lose" coverage here, but otherwise merging NON_REF AD counts with other alleles "creates" reads
+        }
+        return newAnnot;
+    }
+
 
     /**
      *  Remove alternate alleles from a set of genotypes turning removed alleles to no-call and dropping other per-allele attributes
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 fe325bf52a8..3db96575313 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
@@ -184,6 +184,8 @@ public final class ReblockGVCF extends MultiVariantWalker {
 
     private CachingIndexedFastaSequenceFile referenceReader;
 
+    private static final List<String> alleleBasedLengthAnnots = new ArrayList<>();
+
     public static class AlleleLengthComparator implements Comparator<Allele> {
         public int compare(Allele a1, Allele a2) {
             return a1.getBaseString().length() - a2.getBaseString().length();
@@ -256,6 +258,15 @@ public void onTraversalStart() {
             }
         }
 
+        //Allele length and Genotype length annotations need to be subset or removed if alleles are dropped so we need to parse the header for annotation count types
+        for(final VCFFormatHeaderLine formatHeaderLine : inputHeader.getFormatHeaderLines()) {
+            if(formatHeaderLine.getCountType().equals(VCFHeaderLineCount.A) ||
+                    formatHeaderLine.getCountType().equals(VCFHeaderLineCount.R) ||
+                    formatHeaderLine.getCountType().equals(VCFHeaderLineCount.G)) {
+                alleleBasedLengthAnnots.add(formatHeaderLine.getID());
+            }
+        }
+
         if ( dbsnp.dbsnp != null  ) {
             VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.DBSNP_KEY);
         }
@@ -599,7 +610,7 @@ VariantContext cleanUpHighQualityVariant(final VariantContext variant) {
         if(allelesNeedSubsetting && !keepAllAlts) {
             newAlleleSetUntrimmed.removeAll(allelesToDrop);
             final GenotypesContext gc = AlleleSubsettingUtils.subsetAlleles(variant.getGenotypes(), genotype.getPloidy(), variant.getAlleles(),
-                    newAlleleSetUntrimmed, null, GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN);
+                    newAlleleSetUntrimmed, null, GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN, alleleBasedLengthAnnots);
             if (gc.get(0).isHomRef() || !gc.get(0).hasGQ() || gc.get(0).getAlleles().contains(Allele.NO_CALL)) {  //could be low quality or no-call after subsetting
                 if (dropLowQuals) {
                     return null;
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java
index 8ead53254e0..dae22632611 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java
@@ -517,4 +517,38 @@ public void testTreeScoreWithNoAnnotation() {
 
         Assert.assertThrows(UserException.class, () -> runCommandLine(args));
     }
+
+    @Test
+    public void testDragenGvcfs() {
+        final File input = getTestFile("dragen.g.vcf");
+        final File output = createTempFile("reblockedgvcf", ".vcf");
+
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.addReference(new File(hg38Reference))
+                .add("V", input)
+                .add("L", "chr1:939436")
+                .addOutput(output);
+        runCommandLine(args);
+
+        final VCFHeader outHeader = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath()).getLeft();
+        final VariantContext outVC = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath()).getRight().get(0);
+        // The extra allele was dropped so this site is now one alt allele and the <NON_REF> allele
+        Assert.assertEquals(outVC.getAlternateAlleles().size(), 2);
+        final Genotype g = outVC.getGenotype(0);
+        Assert.assertEquals(g.getExtendedAttribute(GATKVCFConstants.ALLELE_FRACTION_KEY),"1.00,0.00");
+        Assert.assertEquals(g.getExtendedAttribute(GATKVCFConstants.F1R2_KEY), "0,3,0");
+        Assert.assertEquals(g.getExtendedAttribute(GATKVCFConstants.F2R1_KEY), "0,3,0");
+        for (String attribute : g.getExtendedAttributes().keySet()) {
+            final VCFHeaderLineCount countType = outHeader.getFormatHeaderLine(attribute).getCountType();
+            if (countType.equals(VCFHeaderLineCount.A)) {
+                Assert.assertEquals(((String) g.getExtendedAttribute(attribute)).split(",").length, 2);
+            }
+            if (countType.equals(VCFHeaderLineCount.R)) {
+                Assert.assertEquals(((String) g.getExtendedAttribute(attribute)).split(",").length, 3);
+            }
+            if (countType.equals(VCFHeaderLineCount.G)) {
+                Assert.assertEquals(((String) g.getExtendedAttribute(attribute)).split(",").length, 6);
+            }
+        }
+    }
 }
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/dragen.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/dragen.g.vcf
new file mode 100644
index 00000000000..bf0779f964a
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/dragen.g.vcf
@@ -0,0 +1,3410 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=DRAGENHardQUAL,Description="Set if true:QUAL<5.0">
+##FILTER=<ID=LowDepth,Description="Set if true:DP<=1">
+##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
+##FILTER=<ID=RMxNRepeatRegion,Description="Site filtered because all or part of the variant allele is a repeat of the reference">
+##FILTER=<ID=base_quality,Description="Site filtered because median base quality of alt reads at this locus does not meet threshold">
+##FILTER=<ID=lod_fstar,Description="Variant does not meet likelihood threshold (default threshold is 6.3)">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (counting only informative reads out of the total reads) for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions for 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=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Phred-scaled posterior probabilities for genotypes as defined in the VCF specification">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=ICNT,Number=2,Type=Integer,Description="Counts of INDEL informative reads based on the reference confidence model">
+##FORMAT=<ID=MB,Number=4,Type=Integer,Description="Per-sample component statistics to detect mate bias">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP 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=PRI,Number=G,Type=Float,Description="Phred-scaled prior probabilities for genotypes">
+##FORMAT=<ID=PS,Number=1,Type=Integer,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=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias">
+##FORMAT=<ID=SPL,Number=.,Type=Integer,Description="Normalized, Phred-scaled likelihoods for SNPs based on the reference confidence model">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Somatic quality">
+##GVCFBlock=minGQ=0(inclusive),maxGQ=20(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=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##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=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=FractionInformativeReads,Number=1,Type=Float,Description="The fraction of informative reads out of the total reads">
+##INFO=<ID=LOD,Number=1,Type=Float,Description="Variant LOD score">
+##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=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=R2_5P_bias,Number=1,Type=Float,Description="Score based on mate bias and distance from 5 prime end">
+##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=chr1,length=248956422>
+##contig=<ID=chr2,length=242193529>
+##contig=<ID=chr3,length=198295559>
+##contig=<ID=chr4,length=190214555>
+##contig=<ID=chr5,length=181538259>
+##contig=<ID=chr6,length=170805979>
+##contig=<ID=chr7,length=159345973>
+##contig=<ID=chr8,length=145138636>
+##contig=<ID=chr9,length=138394717>
+##contig=<ID=chr10,length=133797422>
+##contig=<ID=chr11,length=135086622>
+##contig=<ID=chr12,length=133275309>
+##contig=<ID=chr13,length=114364328>
+##contig=<ID=chr14,length=107043718>
+##contig=<ID=chr15,length=101991189>
+##contig=<ID=chr16,length=90338345>
+##contig=<ID=chr17,length=83257441>
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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/dragen.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/dragen.g.vcf.idx
new file mode 100644
index 00000000000..2b98576b092
Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/dragen.g.vcf.idx differ