diff --git a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java
index 6255f5c82..b314b7a64 100644
--- a/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java
+++ b/src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java
@@ -38,16 +38,14 @@
  * individual.
  *
  * @author Tim Fennell
+ *
+ * @deprecated 6/6/2017 Use {@link CrosscheckFingerprints} instead.
  */
 @CommandLineProgramProperties(
         usage = "DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups within a set of BAM files appear to come from the same individual",
         usageShort = "DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups appear to come from the same individual.",
         programGroup = Fingerprinting.class
 )
-/**
- @deprecated 6/6/2017
- Use  {@link CrosscheckFingerprints} instead.
- */
 @Deprecated
 public class CrosscheckReadGroupFingerprints extends CrosscheckFingerprints {
 
@@ -60,6 +58,11 @@
             "and print out a library x library matrix with LOD scores.")
     public boolean CROSSCHECK_LIBRARIES = false;
 
+    @Option(doc = "Expect all read groups' fingerprints to match, irrespective of their sample names.  By default (with this value set to " +
+            "false), read groups with different sample names are expected to mismatch, and those with the same sample name are expected " +
+            "to match.", mutex = {"EXPECT_ALL_GROUPS_TO_MATCH"})
+    public boolean EXPECT_ALL_READ_GROUPS_TO_MATCH = false;
+
     @Override
     protected String[] customCommandLineValidation() {
         final List<String> errors = new ArrayList<>();
@@ -86,6 +89,10 @@
     @Override
     protected int doWork() {
 
+        if (EXPECT_ALL_READ_GROUPS_TO_MATCH) {
+            EXPECT_ALL_GROUPS_TO_MATCH = EXPECT_ALL_READ_GROUPS_TO_MATCH;
+        }
+
         if (CROSSCHECK_LIBRARIES) {
             CROSSCHECK_BY = CrosscheckMetric.DataType.LIBRARY;
         } else if (CROSSCHECK_SAMPLES) {