diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 734ade376..dc5dfc907 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -129,6 +129,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     @Argument(fullName = "permitNoSampleOverlap", shortName = "permitNoSampleOverlap", doc = "Don't exit (just WARN) when the VCF and BAMs do not overlap in samples", required = false)
     private boolean permitNoSampleOverlap = false;
 
+    @Argument(fullName = "respectPhaseInInput", shortName = "respectPhaseInInput", doc = "Will only phase genotypes in cases where the resulting output will necessarily be consistent with any existing phase (for example, from trios)", required = false)
+    private boolean respectPhaseInInput = false;
+
     private GenomeLoc mostDownstreamLocusReached = null;
 
     private LinkedList<VariantAndReads> unphasedSiteQueue = null;
@@ -487,6 +490,13 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         private int phasingSiteIndex = -1;
         private Map<String, PhasingRead> readsAtHetSites = null;
 
+        private void clearFields() {
+            hetGenotypes = null;
+            prevHetAndInteriorIt = null;
+            phasingSiteIndex = -1;
+            readsAtHetSites = null;
+        }
+
         public boolean hasPreviousHets() {
             return phasingSiteIndex > 0;
         }
@@ -513,12 +523,20 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
             }
             phasingSiteIndex = listHetGenotypes.size();
             if (phasingSiteIndex == 0) { // no previous sites against which to phase
-                hetGenotypes = null;
-                prevHetAndInteriorIt = null;
+                clearFields();
                 return;
             }
             prevHetAndInteriorIt.previous(); // so that it points to the previous het site [and NOT one after it, due to the last call to next()]
 
+            if (respectPhaseInInput) {
+                Genotype prevHetGenotype = prevHetAndInteriorIt.clone().next().unfinishedVariant.getGenotype(sample);
+                if (!prevHetGenotype.isPhased()) {
+                    // Make this genotype unphaseable, since its previous het is not already phased [as required by respectPhaseInInput]:
+                    clearFields();
+                    return;
+                }
+            }
+
             // Add the (het) position to be phased:
             GenomeLoc phaseLocus = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vr.variant);
             GenotypeAndReadBases grbPhase = new GenotypeAndReadBases(vr.variant.getGenotype(sample), vr.sampleReadBases.get(sample), phaseLocus);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
index e1d22f107..b78e76e07 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@@ -80,4 +80,24 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }
 
+    @Test
+    public void test7() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
+                        + " -L chr20:332341-802503",
+                1,
+                Arrays.asList("c37548b333b65f58d0edfc5c2a62a28a"));
+        executeTest("Use trio-phased VCF, but ignore its phasing [TEST SEVEN]", spec);
+    }
+
+    @Test
+    public void test8() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
+                        + " -L chr20:332341-802503" + " -respectPhaseInInput",
+                1,
+                Arrays.asList("dfc7cdddd702e63d46d04f61a3ecd720"));
+        executeTest("Use trio-phased VCF, and respect its phasing [TEST EIGHT]", spec);
+    }
+
 }