diff --git a/src/main/java/picard/sam/AbstractAlignmentMerger.java b/src/main/java/picard/sam/AbstractAlignmentMerger.java
index 484a9b568..ec4dfae50 100644
--- a/src/main/java/picard/sam/AbstractAlignmentMerger.java
+++ b/src/main/java/picard/sam/AbstractAlignmentMerger.java
@@ -58,6 +58,8 @@
 
 import java.io.File;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
 
 /**
@@ -590,11 +592,10 @@ private void transferAlignmentInfoToPairedRead(final SAMRecord firstUnaligned, f
      * Checks to see whether the ends of the reads overlap and soft clips reads
      * them if necessary.
      */
-    protected void clipForOverlappingReads(final SAMRecord read1, final SAMRecord read2) {
+    protected static void clipForOverlappingReads(final SAMRecord read1, final SAMRecord read2) {
         // If both reads are mapped, see if we need to clip the ends due to small
         // insert size
         if (!(read1.getReadUnmappedFlag() || read2.getReadUnmappedFlag())) {
-
             if (read1.getReadNegativeStrandFlag() != read2.getReadNegativeStrandFlag()) {
                 final SAMRecord pos = (read1.getReadNegativeStrandFlag()) ? read2 : read1;
                 final SAMRecord neg = (read1.getReadNegativeStrandFlag()) ? read1 : read2;
@@ -605,23 +606,35 @@ protected void clipForOverlappingReads(final SAMRecord read1, final SAMRecord re
                     final int negDiff = pos.getAlignmentStart() - neg.getAlignmentStart();
 
                     if (posDiff > 0) {
-                        CigarUtil.softClip3PrimeEndOfRead(pos, Math.min(pos.getReadLength(),
-                                pos.getReadLength() - posDiff + 1));
+                        final List<CigarElement> elems = new ArrayList<>(pos.getCigar().getCigarElements());
+                        Collections.reverse(elems);
+                        final int clipped = lengthOfSoftClipping(elems.iterator());
+                        final int clipFrom = pos.getReadLength() - posDiff - clipped + 1;
+                        CigarUtil.softClip3PrimeEndOfRead(pos, Math.min(pos.getReadLength(), clipFrom));
                         removeNmMdAndUqTags(pos); // these tags are now invalid!
                     }
 
                     if (negDiff > 0) {
-                        CigarUtil.softClip3PrimeEndOfRead(neg, Math.min(neg.getReadLength(),
-                                neg.getReadLength() - negDiff + 1));
+                        final int clipped = lengthOfSoftClipping(neg.getCigar().getCigarElements().iterator());
+                        final int clipFrom = neg.getReadLength() - negDiff - clipped + 1;
+                        CigarUtil.softClip3PrimeEndOfRead(neg, Math.min(neg.getReadLength(), clipFrom));
                         removeNmMdAndUqTags(neg); // these tags are now invalid!
                     }
-
                 }
-            } else {
-                // TODO: What about RR/FF pairs?
             }
         }
+    }
+
+    /** Returns the number of soft-clipped bases until a non-soft-clipping element is encountered. */
+    private static int lengthOfSoftClipping(Iterator<CigarElement> iterator) {
+        int clipped = 0;
+        while (iterator.hasNext()) {
+            final CigarElement elem = iterator.next();
+            if (elem.getOperator() != CigarOperator.SOFT_CLIP && elem.getOperator() != CigarOperator.HARD_CLIP) break;
+            if (elem.getOperator() == CigarOperator.SOFT_CLIP) clipped = elem.getLength();
+        }
 
+        return clipped;
     }
 
     /**
diff --git a/src/test/java/picard/sam/AbstractAlignmentMergerTest.java b/src/test/java/picard/sam/AbstractAlignmentMergerTest.java
new file mode 100644
index 000000000..828d1c466
--- /dev/null
+++ b/src/test/java/picard/sam/AbstractAlignmentMergerTest.java
@@ -0,0 +1,65 @@
+package picard.sam;
+
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SAMRecordSetBuilder;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.util.List;
+
+/**
+ * Tests related to code in AbstractAlignmentMerger
+ */
+public class AbstractAlignmentMergerTest {
+    @Test public void tesOverlappedReadClippingWithNonOverlappedReads() {
+        final SAMRecordSetBuilder set = new SAMRecordSetBuilder();
+        set.setReadLength(110);
+        final List<SAMRecord> recs = set.addPair("q1", 0, 100, 200, false, false, "110M", "110M", false, true, 30);
+        final SAMRecord r1 = recs.get(0);
+        final SAMRecord r2 = recs.get(1);
+        AbstractAlignmentMerger.clipForOverlappingReads(r1, r2);
+        Assert.assertEquals(r1.getAlignmentStart(), 100);
+        Assert.assertEquals(r1.getCigarString(), "110M");
+        Assert.assertEquals(r2.getAlignmentStart(), 200);
+        Assert.assertEquals(r2.getCigarString(), "110M");
+    }
+
+    @Test public void testBasicOverlappedReadClipping() {
+        final SAMRecordSetBuilder set = new SAMRecordSetBuilder();
+        set.setReadLength(110);
+        final List<SAMRecord> recs = set.addPair("q1", 0, 100, 90, false, false, "110M", "110M", false, true, 30);
+        final SAMRecord r1 = recs.get(0);
+        final SAMRecord r2 = recs.get(1);
+        AbstractAlignmentMerger.clipForOverlappingReads(r1, r2);
+        Assert.assertEquals(r1.getAlignmentStart(), 100);
+        Assert.assertEquals(r1.getCigarString(), "100M10S");
+        Assert.assertEquals(r2.getAlignmentStart(), 100);
+        Assert.assertEquals(r2.getCigarString(), "10S100M");
+    }
+
+    @Test public void testOverlappedReadClippingWithExistingSoftClipping() {
+        final SAMRecordSetBuilder set = new SAMRecordSetBuilder();
+        set.setReadLength(120);
+        final List<SAMRecord> recs = set.addPair("q1", 0, 100, 95, false, false, "110M10S", "15S105M", false, true, 30);
+        final SAMRecord r1 = recs.get(0);
+        final SAMRecord r2 = recs.get(1);
+        AbstractAlignmentMerger.clipForOverlappingReads(r1, r2);
+        Assert.assertEquals(r1.getAlignmentStart(), 100);
+        Assert.assertEquals(r1.getCigarString(), "100M20S");
+        Assert.assertEquals(r2.getAlignmentStart(), 100);
+        Assert.assertEquals(r2.getCigarString(), "20S100M");
+    }
+
+    @Test public void testOverlappedReadClippingWithExistingSoftClippingAndHardClipping() {
+        final SAMRecordSetBuilder set = new SAMRecordSetBuilder();
+        set.setReadLength(120);
+        final List<SAMRecord> recs = set.addPair("q1", 0, 100, 95, false, false, "110M10S5H", "5H15S105M", false, true, 30);
+        final SAMRecord r1 = recs.get(0);
+        final SAMRecord r2 = recs.get(1);
+        AbstractAlignmentMerger.clipForOverlappingReads(r1, r2);
+        Assert.assertEquals(r1.getAlignmentStart(), 100);
+        Assert.assertEquals(r1.getCigarString(), "100M20S"); // Should ideally be 100M20S5H
+        Assert.assertEquals(r2.getAlignmentStart(), 100);
+        Assert.assertEquals(r2.getCigarString(), "20S100M"); // Should ideally be 5H20S100M
+    }
+}