diff --git a/src/main/java/org/broadinstitute/hellbender/engine/filters/CountingVariantFilter.java b/src/main/java/org/broadinstitute/hellbender/engine/filters/CountingVariantFilter.java
index ce1a507871b..f9d15210ef2 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/filters/CountingVariantFilter.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/filters/CountingVariantFilter.java
@@ -17,7 +17,7 @@
  * (ie., not all variant filters in a compound predicate will necessarily be evaluated every time). Also note
  * that the count for a compound predicate does not always equal the sum of the counts of it's component
  * predicates, i.e. an "or" filter will report a filter count of 1 in the case where both component predicates
- * are evaluated and both fail, but the the individual component filters will report a count of 1 at the next
+ * are evaluated and both fail, but the individual component filters will report a count of 1 at the next
  * level.
  */
 public class CountingVariantFilter implements VariantFilter {
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java
index c0ac67c177b..ac353d1878c 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java
@@ -266,6 +266,7 @@ public static AssemblyResultSet assembleReads(final AssemblyRegion region,
             final AssemblyResultSet assemblyResultSet = assemblyEngine.runLocalAssembly(region, referenceHaplotype, fullReferenceWithPadding,
                                                                                         paddedReferenceLoc, givenAlleles, readErrorCorrector, header,
                                                                                         aligner);
+            assemblyResultSet.setDebug(argumentCollection.debug);
             assemblyResultSet.debugDump(logger);
             return assemblyResultSet;
         } catch (final Exception e){
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResultSet.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResultSet.java
index 4e0e2eeed46..b05934e3620 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResultSet.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyResultSet.java
@@ -518,4 +518,8 @@ public SortedSet<VariantContext> getVariationEvents(final int maxMnpDistance) {
         }
         return variationEvents;
     }
+
+    public void setDebug(boolean debug) {
+        this.debug = debug;
+    }
 }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
index ee248b90c5e..5b114e03daf 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
@@ -536,7 +536,7 @@ public List<VariantContext> callRegion(final AssemblyRegion region, final Featur
 
         // run the local assembler, getting back a collection of information on how we should proceed
         final AssemblyResultSet untrimmedAssemblyResult =  AssemblyBasedCallerUtils.assembleReads(region, givenAlleles, hcArgs, readsHeader, samplesList, logger, referenceReader, assemblyEngine, aligner);
-
+        
         final SortedSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents(hcArgs.maxMnpDistance);
         // TODO - line bellow might be unnecessary : it might be that assemblyResult will always have those alleles anyway
         // TODO - so check and remove if that is the case:
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java
index c552344b722..209e381fc1b 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java
@@ -193,6 +193,7 @@ public List<VariantContext> callRegion(final AssemblyRegion originalAssemblyRegi
 
         final AssemblyRegion assemblyActiveRegion = AssemblyBasedCallerUtils.assemblyRegionWithWellMappedReads(originalAssemblyRegion, READ_QUALITY_FILTER_THRESHOLD, header);
         final AssemblyResultSet untrimmedAssemblyResult = AssemblyBasedCallerUtils.assembleReads(assemblyActiveRegion, givenAlleles, MTAC, header, samplesList, logger, referenceReader, assemblyEngine, aligner);
+
         final SortedSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents(MTAC.maxMnpDistance);
         final AssemblyRegionTrimmer.Result trimmingResult = trimmer.trim(originalAssemblyRegion, allVariationEvents);
         if (!trimmingResult.isVariationPresent()) {