diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java
index d9ae3289a..2b81d45c4 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java
@@ -57,7 +57,7 @@ import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardUGAnnotation;
 import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import htsjdk.variant.vcf.VCFConstants;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
@@ -79,7 +79,7 @@ import java.util.Map;
  * <p>This anotation gives you the count of all reads that have MAPQ = 0 across all samples. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.</p>
  *
  * <h3>Caveat</h3>
- * <p>This annotation is excluded by HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation would always return a value of 0 anyway.</p>
+ * <p>It is not useful to apply this annotation with HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation will always return a value of 0.</p>
  *
  * <h3>Related annotations</h3>
  * <ul>
@@ -88,7 +88,7 @@ import java.util.Map;
  * </ul>
  *
  */
-public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
+public class MappingQualityZero extends InfoFieldAnnotation implements StandardUGAnnotation, ActiveRegionBasedAnnotation {
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                         final AnnotatorCompatible walker,
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index 5df2a12fb..76f8cbc2e 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -293,12 +293,16 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     protected List<String> annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"ClippingRankSumTest", "DepthPerSampleHC"}));
 
     /**
-     * Which annotations to exclude from output in the VCF file.  Note that this argument has higher priority than the -A or -G arguments,
-     * so these annotations will be excluded even if they are explicitly included with the other options.
+     * Which annotations to exclude from output in the VCF file.  Note that this argument has higher priority than the
+     * -A or -G arguments, so these annotations will be excluded even if they are explicitly included with the other
+     * options. When HaplotypeCaller is run with -ERC GVCF or -ERC BP_RESOLUTION, some annotations are excluded from the
+     * output by default because they will only be meaningful once they have been recalculated by GenotypeGVCFs. As
+     * of version 3.3 this concerns ChromosomeCounts, FisherStrand, StrandOddsRatio and QualByDepth.
+     *
      */
     @Advanced
     @Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
-    protected List<String> annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{"MappingQualityZero", "MappingQualityZeroBySample"}));
+    protected List<String> annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{}));
 
     /**
      * Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See
@@ -506,7 +510,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         }
 
         if (dontGenotype && emitReferenceConfidence())
-            throw new UserException("You cannot request gVCF output and do not genotype at the same time");
+            throw new UserException("You cannot request gVCF output and 'do not genotype' at the same time");
 
         if ( emitReferenceConfidence() ) {
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
index 13057381e..728fa3fa3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
@@ -50,7 +50,7 @@ import java.util.List;
  * <p>This annotation gives you the count of all reads that have MAPQ = 0 for each sample. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.</p>
  *
  * <h3>Caveat</h3>
- * <p>This annotation is excluded by HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation would always return a value of 0 anyway.</p>
+ * <p>It is not useful to apply this annotation with HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation will always return a value of 0.</p>
  *
  * <h3>Related annotations</h3>
  * <ul>