diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java
index 2b681a440..ae9c0a5bc 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java
@@ -241,6 +241,8 @@ public class EmpiricalSubstitutionGenotypeLikelihoods extends GenotypeLikelihood
         return EMPIRICAL_CACHE[a][i][j][k][x];
     }
   
+    protected void clearCache() { EMPIRICAL_CACHE = new GenotypeLikelihoods[EmpiricalSubstitutionGenotypeLikelihoods.SequencerPlatform.values().length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE][MAX_PLOIDY][2]; }
+
 
     // -----------------------------------------------------------------------------------------------------------------
     //
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
index 7e7de302c..17a351396 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
@@ -78,7 +78,12 @@ public abstract class GenotypeLikelihoods implements Cloneable {
         initialize();
     }
 
-    public static GenotypeLikelihoods merge(GenotypeLikelihoods gl1, GenotypeLikelihoods gl2) {
+    public static GenotypeLikelihoods combineLikelihoods(GenotypeLikelihoods gl1, GenotypeLikelihoods gl2) {
+        if ( gl1 == null )
+            return gl2;
+        if ( gl2 == null )
+            return gl1;
+
         // GL = GL_i + GL_j
 
         GenotypeLikelihoods gl;
@@ -182,6 +187,14 @@ public abstract class GenotypeLikelihoods implements Cloneable {
         return priors.getPriors();
     }
 
+    /**
+     * Sets the priors and clears the likelihoods cache.
+     */
+    public void setPriors(DiploidGenotypePriors priors) {
+        this.priors = priors;
+        clearCache();
+    }
+
     /**
      * Returns the prior associated with DiploidGenotype g
      * @param g
@@ -334,6 +347,10 @@ public abstract class GenotypeLikelihoods implements Cloneable {
      */
     protected abstract GenotypeLikelihoods getSetCache( char observedBase, byte qualityScore, int ploidy,
                                                         SAMRecord read, int offset, GenotypeLikelihoods val );
+    /**
+     * Method for clearing the cache (in case we change the priors)
+     */
+    protected abstract void clearCache();
 
     protected GenotypeLikelihoods simpleGetSetCache( GenotypeLikelihoods[][][][] cache,
                                                      char observedBase, byte qualityScore, int ploidy,
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ThreeStateErrorGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ThreeStateErrorGenotypeLikelihoods.java
index fde835d3d..bda9481b6 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ThreeStateErrorGenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ThreeStateErrorGenotypeLikelihoods.java
@@ -40,4 +40,5 @@ public class ThreeStateErrorGenotypeLikelihoods extends GenotypeLikelihoods {
                                              SAMRecord read, int offset, GenotypeLikelihoods val ) {
         return simpleGetSetCache(THREE_STATE_CACHE, observedBase, qualityScore, ploidy, read, offset, val);
     }
+    protected void clearCache() { THREE_STATE_CACHE = new GenotypeLikelihoods[BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE][MAX_PLOIDY][2]; }
 }