diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
index bc7c5a1ce..f3d4a3096 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
@@ -188,7 +188,7 @@ public class BaseRecalibration {
         }
     }
 
-    protected double hierarchicalBayesianQualityEstimate( final double epsilon, final RecalDatum empiricalQualRG, final RecalDatum empiricalQualQS, final List<RecalDatum> empiricalQualCovs ) {
+    protected static double hierarchicalBayesianQualityEstimate( final double epsilon, final RecalDatum empiricalQualRG, final RecalDatum empiricalQualQS, final List<RecalDatum> empiricalQualCovs ) {
         final double globalDeltaQ = ( empiricalQualRG == null ? 0.0 : empiricalQualRG.getEmpiricalQuality(epsilon) - epsilon );
         final double deltaQReported = ( empiricalQualQS == null ? 0.0 : empiricalQualQS.getEmpiricalQuality(globalDeltaQ + epsilon) - (globalDeltaQ + epsilon) );
         double deltaQCovariates = 0.0;
diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
index 0b4441439..bd0063a7d 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
@@ -181,6 +181,7 @@ public class RecalDatum {
         if ( Double.isNaN(estimatedQReported) ) throw new IllegalArgumentException("estimatedQReported is NaN");
 
         this.estimatedQReported = estimatedQReported;
+        empiricalQuality = UNINITIALIZED;
     }
 
     public final double getEstimatedQReported() {
diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
index 2f9a38972..f10c26ddc 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
@@ -131,7 +131,7 @@ public class RecalibrationReport {
     * Combines two recalibration reports by adding all observations and errors
     *
     * Note: This method DOES NOT recalculate the empirical qualities and quantized qualities. You have to recalculate
-    * them after combining. The reason for not calculating it is because this function is inteded for combining a
+    * them after combining. The reason for not calculating it is because this function is intended for combining a
     * series of recalibration reports, and it only makes sense to calculate the empirical qualities and quantized
     * qualities after all the recalibration reports have been combined. Having the user recalculate when appropriate,
     * makes this method faster
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java
index 2815599d9..f82f24439 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java
@@ -125,19 +125,19 @@ public class BQSRGathererUnitTest extends BaseTest {
         testTablesWithColumns(originalTable, calculatedTable, columnsToTest);
 
         // test the RecalTable0 table
-        columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
+        columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
         originalTable = originalReport.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE);
         calculatedTable = calculatedReport.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE);
         testTablesWithColumns(originalTable, calculatedTable, columnsToTest);
 
         // test the RecalTable1 table
-        columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.QUALITY_SCORE_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
+        columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.QUALITY_SCORE_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
         originalTable = originalReport.getTable(RecalUtils.QUALITY_SCORE_REPORT_TABLE_TITLE);
         calculatedTable = calculatedReport.getTable(RecalUtils.QUALITY_SCORE_REPORT_TABLE_TITLE);
         testTablesWithColumns(originalTable, calculatedTable, columnsToTest);
 
         // test the RecalTable2 table
-        columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.QUALITY_SCORE_COLUMN_NAME, RecalUtils.COVARIATE_VALUE_COLUMN_NAME, RecalUtils.COVARIATE_NAME_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
+        columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.QUALITY_SCORE_COLUMN_NAME, RecalUtils.COVARIATE_VALUE_COLUMN_NAME, RecalUtils.COVARIATE_NAME_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME);
         originalTable = originalReport.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE);
         calculatedTable = calculatedReport.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE);
         testTablesWithColumns(originalTable, calculatedTable, columnsToTest);
diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
index 09f751fbc..37f0fcc0c 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
@@ -58,6 +58,7 @@ import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
+import java.util.Collections;
 
 
 public class RecalDatumUnitTest extends BaseTest {
@@ -277,4 +278,36 @@ public class RecalDatumUnitTest extends BaseTest {
         Assert.assertFalse(Double.isInfinite(log10likelihood));
         Assert.assertFalse(Double.isNaN(log10likelihood));
     }
+
+    @Test
+    public void basicHierarchicalBayesianQualityEstimateTest() {
+        {
+            double RG_Q = 45.0;
+            RecalDatum RG = new RecalDatum( (long)10000000, (long) (10000000 * 1.0 / (Math.pow(10.0, RG_Q/10.0))), (byte)RG_Q);
+            double Q = 30.0;
+            RecalDatum QS = new RecalDatum( (long)10000000, (long) (10000000 * 1.0 / (Math.pow(10.0, Q/10.0))), (byte)Q);
+            RecalDatum COV = new RecalDatum( (long)150, (long) 1, (byte)45.0); // no data here so Bayesian prior has a huge effect on the empirical quality
+
+            Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( 45.0, RG, QS, Collections.singletonList(COV)), Q, 1E-4 );
+            // initial epsilon condition shouldn't matter when there are a lot of observations
+            Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( 25.0, RG, QS, Collections.singletonList(COV)), Q, 1E-4 );
+            Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( 5.0, RG, QS, Collections.singletonList(COV)), Q, 1E-4 );
+            Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( 65.0, RG, QS, Collections.singletonList(COV)), Q, 1E-4 );
+        }
+
+        {
+            double RG_Q = 45.0;
+            RecalDatum RG = new RecalDatum( (long)100, (long) (100 * 1.0 / (Math.pow(10.0, RG_Q/10.0))), (byte)RG_Q);
+            double Q = 30.0;
+            RecalDatum QS = new RecalDatum( (long)100, (long) (100 * 1.0 / (Math.pow(10.0, Q/10.0))), (byte)Q);
+            RecalDatum COV = new RecalDatum( (long)150, (long) 1, (byte)45.0); // no data here so Bayesian prior has a huge effect on the empirical quality
+
+            // initial epsilon condition dominates when there is no data
+            Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( 45.0, RG, QS, Collections.singletonList(COV)), 45.0, 1E-4 );
+            Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( 25.0, RG, QS, Collections.singletonList(COV)), 25.0, 1E-4 );
+            Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( 5.0, RG, QS, Collections.singletonList(COV)), 5.0, 1E-4 );
+            Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( 65.0, RG, QS, Collections.singletonList(COV)), 65.0, 1E-4 );
+        }
+
+    }
 }
\ No newline at end of file