diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java
index 07c7bfc8e..ae7057de3 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java
@@ -40,8 +40,8 @@ import org.broadinstitute.gatk.utils.exceptions.UserException;
  *     This filter is intended to filter out reads that are potentially from foreign organisms.
  *     From experience with sequencing of human DNA we have found cases of contamination by bacterial
  *     organisms; the symptoms of such contamination are a class of reads with only a small number
- *     of aligned bases and additionally many soft-clipped bases on both ends.  This filter is intended
- *     to remove such reads.
+ *     of aligned bases and additionally many soft-clipped bases.  This filter is intended
+ *     to remove such reads. Consecutive soft-clipped blocks are treated as a single block
  * </p>
  *
  */
@@ -50,25 +50,31 @@ public class OverclippedReadFilter extends ReadFilter {
     @Argument(fullName = "filter_is_too_short_value", shortName = "filterTooShort", doc = "Value for which reads with less than this number of aligned bases is considered too short", required = false)
     int tooShort = 30;
 
+    @Argument(fullName = "do_not_require_softclips_both_ends", shortName = "NoRequireSCBothEnds", doc = "Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block.", required = false)
+    Boolean doNotRequireSoftclipsOnBothEnds = false;
+
 
     public boolean filterOut(final SAMRecord read) {
-        boolean sawLeadingSoftclip = false;
-        boolean sawAlignedBase = false;
         int alignedLength = 0;
+        int softClipBlocks = 0;
+        int minSoftClipBlocks = doNotRequireSoftclipsOnBothEnds ? 1 : 2;
+        CigarOperator lastOperator = null;
 
         for ( final CigarElement element : read.getCigar().getCigarElements() ) {
             if ( element.getOperator() == CigarOperator.S ) {
-                if ( sawAlignedBase )  // if this is true then we must also have seen a leading soft-clip
-                    return (alignedLength < tooShort);
-                sawLeadingSoftclip = true;
+                //Treat consecutive S blocks as a single one
+                if(lastOperator != CigarOperator.S){
+                    softClipBlocks += 1;
+                }
+
             } else if ( element.getOperator().consumesReadBases() ) {   // M, I, X, and EQ (S was already accounted for above)
-                if ( !sawLeadingSoftclip )
-                    return false;
-                sawAlignedBase = true;
                 alignedLength += element.getLength();
             }
+            lastOperator = element.getOperator();
         }
 
-        return false;
+        return(alignedLength < tooShort && softClipBlocks >= minSoftClipBlocks);
+
     }
+
 }
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java
index 3400b61e9..85d95b5f2 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java
@@ -42,11 +42,12 @@ import java.util.*;
 public class OverclippedReadFilterUnitTest extends ReadFilterTest {
 
     @Test(enabled = true, dataProvider= "OverclippedDataProvider")
-    public void testOverclippedFilter(final String cigarString, final boolean expectedResult) {
+    public void testOverclippedFilter(final String cigarString, boolean doNotRequireSoftclipsOnBothEnds, final boolean expectedResult) {
 
-       final OverclippedReadFilter filter = new OverclippedReadFilter();
-       final SAMRecord read = buildSAMRecord(cigarString);
-       Assert.assertEquals(filter.filterOut(read), expectedResult, cigarString);
+        final OverclippedReadFilter filter = new OverclippedReadFilter();
+        filter.doNotRequireSoftclipsOnBothEnds = doNotRequireSoftclipsOnBothEnds;
+        final SAMRecord read = buildSAMRecord(cigarString);
+        Assert.assertEquals(filter.filterOut(read), expectedResult, cigarString);
     }
 
     private SAMRecord buildSAMRecord(final String cigarString) {
@@ -58,20 +59,47 @@ public class OverclippedReadFilterUnitTest extends ReadFilterTest {
     public Iterator<Object[]> overclippedDataProvider() {
         final List<Object[]> result = new LinkedList<Object[]>();
 
-        result.add(new Object[] { "1S10M1S", true });
-        result.add(new Object[] { "1S10X1S", true });
-        result.add(new Object[] { "1H1S10M1S1H", true });
-        result.add(new Object[] { "1S40M1S", false });
-        result.add(new Object[] { "1S40X1S", false });
-        result.add(new Object[] { "1H10M1S", false });
-        result.add(new Object[] { "1S10M1H", false });
-        result.add(new Object[] { "10M1S", false });
-        result.add(new Object[] { "1S10M", false });
-        result.add(new Object[] { "1S10M10D10M1S", true });
-        result.add(new Object[] { "1S1M40I1S", false });
-        result.add(new Object[] { "1S10I1S", true });
-        result.add(new Object[] { "1S40I1S", false });
+        result.add(new Object[] { "1S10M1S", false, true });
+        result.add(new Object[] { "1S10X1S", false, true });
+        result.add(new Object[] { "1H1S10M1S1H", false, true });
+        result.add(new Object[] { "1S40M1S", false, false});
+        result.add(new Object[] { "1S40X1S", false, false });
+        result.add(new Object[] { "1H10M1S", false, false});
+        result.add(new Object[] { "1S10M1H", false, false});
+
+        result.add(new Object[] { "10M1S", false, false});
+        result.add(new Object[] { "1S10M", false, false});
+
+        result.add(new Object[] { "10M1S", true, true});
+        result.add(new Object[] { "1S10M", true, true});
+
+        result.add(new Object[] { "1S10M10D10M1S", false, true });
+        result.add(new Object[] { "1S1M40I1S", false, false });
+
+        result.add(new Object[] { "1S10I1S", false, true });
+        result.add(new Object[] { "1S40I1S", false, false });
+        result.add(new Object[] { "1S40I1S", true, false });
+
+        result.add(new Object[] { "25S40I25M", true, false });
+
+        //Read is too short once soft-clipping removed
+        result.add(new Object[] { "25S25M", true, true });
+        result.add(new Object[] { "25S25X", true, true });
+        result.add(new Object[] { "25S25H", true, true });
+        result.add(new Object[] { "25S25H", false, false });
+
+        result.add(new Object[] { "25S25M25S", false, true });
+        result.add(new Object[] { "25M25S", true, true });
+        result.add(new Object[] { "25S25M", true, true });
+
+        result.add(new Object[] { "25S35S", true, true });
+
+        //Read long enough even with soft clipping removed
+        result.add(new Object[] { "25S35M25S", true, false });
+        result.add(new Object[] { "35M25S", true, false });
+        result.add(new Object[] { "25S35M", true, false });
 
         return result.iterator();
     }
+
 }