Why not just make 10 louder?

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java

@@ -10,7 +10,9 @@
 import htsjdk.variant.vcf.VCFStandardHeaderLines;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.help.DocumentedFeature;
+import org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.ReferenceContext;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation;
@@ -55,6 +57,10 @@ public final class RMSMappingQuality extends InfoFieldAnnotation implements Stan
     public static final int NUM_LIST_ENTRIES = 2;
     public static final int SUM_OF_SQUARES_INDEX = 0;
     public static final int TOTAL_DEPTH_INDEX = 1;
+    public static final String RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT = "allow-old-rms-mapping-quality-annotation-data";
+
+    @Argument(fullName = RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT, doc="Override to allow old RMSMappingQuality annotatated VCFs to function", optional=true)
+    public boolean allowOlderRawKeyValues = false;
 
     @Override
     public String getRawKeyName() { return GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY;}   //new key for the two-value MQ data to prevent version mismatch catastrophes
@@ -124,6 +130,13 @@ public Map<String, Object> finalizeRawData(final VariantContext vc, final Varian
             rawMQdata = vc.getAttributeAsString(getRawKeyName(), null);
         }
         else if (vc.hasAttribute(getDeprecatedRawKeyName())) {
+            if (!allowOlderRawKeyValues) {
+                throw new UserException.BadInput(String.format("Presence of -%s annotation is detected. This GATK version expects key "
+                        + getRawKeyName() + " with an long tuple of sum of squared MQ values and total reads over variant "
+                        + "genotypes as the value. This could indicate that the provided input was produced with an older version of GATK. " +
+                        "Use the argument '--"+RMS_MAPPING_QUALITY_OLD_BEHAVIOR_OVERRIDE_ARGUMENT+"' to override and attempt the depricated MQ calculation."));
+            }
+
             rawMQdata = vc.getAttributeAsString(getDeprecatedRawKeyName(), null);
             //the original version of ReblockGVCF produces a different MQ format -- try to handle that gracefully here just in case those files go through GenotypeGVCFs
             if (vc.hasAttribute("MQ_DP")) {