diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 484981e44..9cf55dee5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -76,6 +76,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     public static final String ORIGINAL_POSITION_TAG = "OP";
     public static final String PROGRAM_RECORD_NAME = "GATK IndelRealigner";
 
+    public enum ConsensusDeterminationModel {
+        KNOWNS_ONLY,
+        USE_READS,
+        USE_SW
+    }
+
     @Input(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
     protected String intervalsFile = null;
 
@@ -89,12 +95,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     protected StingSAMFileWriter writer = null;
     protected ConstrainedMateFixingManager manager = null;
 
-    @Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", required=false, doc="Don't run 'Smith-Waterman' to generate alternate consenses; use only known indels provided as RODs for constructing the alternate references.")
-    protected boolean USE_KNOWN_INDELS_ONLY = false;
-
-    @Hidden
-    @Argument(fullName="doNotUseSW", shortName="doNotUseSW", required=false, doc="Don't run 'Smith-Waterman' to generate alternate consenses; use only known indels provided as RODs or indels in the reads for constructing the alternate references.")
-    protected boolean NO_SW = false;
+    @Argument(fullName = "consensusDeterminationModel", shortName = "model", doc = "How should we determine the possible alternate consenses? -- in the order of least permissive to most permissive there is KNOWNS_ONLY (use only indels from known indels provided in RODs), USE_READS (additionally use indels already present in the original alignments of the reads), and USE_SW (additionally use 'Smith-Waterman' to generate alternate consenses).  The default is USE_SW", required = false)
+    public ConsensusDeterminationModel consensusModel = ConsensusDeterminationModel.USE_SW;
 
 
     // ADVANCED OPTIONS FOLLOW
@@ -646,7 +648,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         long totalRawMismatchSum = determineReadsThatNeedCleaning(reads, refReads, altReads, altAlignmentsToTest, altConsenses, leftmostIndex, reference);
 
         // use 'Smith-Waterman' to create alternate consenses from reads that mismatch the reference, using totalRawMismatchSum as the random seed
-        if ( !USE_KNOWN_INDELS_ONLY && !NO_SW )
+        if ( consensusModel == ConsensusDeterminationModel.USE_SW )
             generateAlternateConsensesFromReads(altAlignmentsToTest, altConsenses, reference, leftmostIndex);
 
         // if ( debugOn ) System.out.println("------\nChecking consenses...\n--------\n");
@@ -723,7 +725,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 if ( !updateRead(bestConsensus.cigar, bestConsensus.positionOnReference, indexPair.second, aRead, leftmostIndex) )
                     return;
             }
-            if ( !USE_KNOWN_INDELS_ONLY && !alternateReducesEntropy(altReads, reference, leftmostIndex) ) {
+            if ( consensusModel != ConsensusDeterminationModel.KNOWNS_ONLY && !alternateReducesEntropy(altReads, reference, leftmostIndex) ) {
                 if ( statsOutput != null ) {
                     try {
                         statsOutput.write(currentInterval.toString());
@@ -885,7 +887,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 aRead.setAlignerMismatchScore(AlignmentUtils.mismatchingQualities(aRead.getRead(), reference, startOnRef));
 
                 // if it has an indel, let's see if that's the best consensus
-                if ( !USE_KNOWN_INDELS_ONLY && numBlocks == 2 )  {
+                if ( consensusModel != ConsensusDeterminationModel.KNOWNS_ONLY && numBlocks == 2 )  {
                     Consensus c = createAlternateConsensus(startOnRef, aRead.getCigar(), reference, aRead.getReadBases());
                     if ( c != null )
                         altConsenses.add(c);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 20edf9b08..3e8ec3e02 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -43,18 +43,33 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
     public void testKnownsOnly() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
-                baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels,
+                baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -B:indels,vcf " + knownIndels,
                 1,
                 Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888"));
         executeTest("realigner known indels only from VCF", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                baseCommand + "-knownsOnly -D " + GATKDataLocation + "dbsnp_129_b36.rod",
+                baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -D " + GATKDataLocation + "dbsnp_129_b36.rod",
                 1,
                 Arrays.asList("78850024ac9ff3ba51b6f097c7041c1d"));
         executeTest("realigner known indels only from dbsnp", spec2);
     }
 
+    @Test
+    public void testReadsOnly() {
+        WalkerTestSpec spec1 = new WalkerTestSpec(
+                baseCommand + "--consensusDeterminationModel USE_READS -B:indels,vcf " + knownIndels,
+                1,
+                Arrays.asList(base_md5));
+        executeTest("realigner known indels only from VCF", spec1);
+
+        WalkerTestSpec spec2 = new WalkerTestSpec(
+                baseCommand + "--consensusDeterminationModel USE_READS -D " + GATKDataLocation + "dbsnp_129_b36.rod",
+                1,
+                Arrays.asList("e041186bca9dccf360747c89be8417ad"));
+        executeTest("realigner known indels only from dbsnp", spec2);
+    }
+
     @Test
     public void testLods() {
         HashMap<String, String> e = new HashMap<String, String>();
diff --git a/scala/qscript/playground/WholeGenomePipeline.scala b/scala/qscript/playground/WholeGenomePipeline.scala
index 344124f71..088528ac0 100644
--- a/scala/qscript/playground/WholeGenomePipeline.scala
+++ b/scala/qscript/playground/WholeGenomePipeline.scala
@@ -149,7 +149,7 @@ class WholeGenomePipeline extends QScript {
         clean.targetIntervals = target.out
         clean.rodBind :+= RodBind("dbsnp", "VCF", dbsnp)
         clean.rodBind :+= RodBind("indels", "VCF", indels)
-        clean.doNotUseSW = true
+        clean.consensusDeterminationModel = org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel.USE_READS
         clean.simplifyBAM = true
         clean.bam_compression = 1
         clean.out = tmpBase + ".cleaned.bam"