diff --git a/src/main/java/picard/analysis/directed/TargetMetricsCollector.java b/src/main/java/picard/analysis/directed/TargetMetricsCollector.java
index fc91fda92..e11a6f234 100644
--- a/src/main/java/picard/analysis/directed/TargetMetricsCollector.java
+++ b/src/main/java/picard/analysis/directed/TargetMetricsCollector.java
@@ -538,7 +538,13 @@ public void acceptRecord(final SAMRecord record) {
                 final int numOverlappingBasesToClip = SAMUtils.getNumOverlappingAlignedBasesToClip(record);
                 rec = SAMUtils.clipOverlappingAlignedBases(record, numOverlappingBasesToClip, noSideEffects);
                 metrics.PCT_EXC_OVERLAP += numOverlappingBasesToClip;
-            } else rec = record;
+
+                // If clipping resulted in the read becoming unmapped (because all bases were clipped), return here
+                if (rec.getReadUnmappedFlag()) return;
+            }
+            else {
+                rec = record;
+            }
 
             // Find the target overlaps
             final Set<Interval> coveredTargets = new HashSet<>();
diff --git a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
index 7ac2b35bb..287d59cfc 100644
--- a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
+++ b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
@@ -32,7 +32,7 @@ public String getCommandLineProgramName() {
                 // test that read 2 (with mapping quality 1) is filtered out with minimum mapping quality 2
                 {TEST_DIR + "/lowmapq.sam",     intervals, 2, 0, true,  2, 202, 0,   0.0, 0.505, 0.0,   1000},
                 // test that we clip overlapping bases
-                {TEST_DIR + "/overlapping.sam", intervals, 0, 0, true,  2, 202, 0,   0.5, 0.505, 0.505, 1000},
+                {TEST_DIR + "/overlapping.sam", intervals, 0, 0, true,  2, 202, 0,   0.5, 0.505, 0, 1000},
                 // test that we do not clip overlapping bases
                 {TEST_DIR + "/overlapping.sam", intervals, 0, 0, false, 2, 202, 0,   0.0, 0.505, 0.505, 1000},
                 // A read 10 base pairs long. two intervals: one maps identically to the read, other does not overlap at all