diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
index fae0e8c09..de1ed5602 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
@@ -14,12 +14,15 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  */
 public class BQSRReadTransformer extends ReadTransformer {
     private boolean enabled;
-    private BaseRecalibration bqsr;
+    private BaseRecalibration bqsr = null;
 
     @Override
     public ApplicationTime initializeSub(final GenomeAnalysisEngine engine, final Walker walker) {
-        this.enabled = engine.hasBaseRecalibration();
-        this.bqsr = engine.getBaseRecalibration();
+        this.enabled = engine.hasBQSRArgumentSet();
+        if ( enabled ) {
+            final BQSRArgumentSet args = engine.getBQSRArgumentSet();
+            this.bqsr = new BaseRecalibration(args.getRecalFile(), args.getQuantizationLevels(), args.shouldDisableIndelQuals(), args.getPreserveQscoresLessThan(), args.shouldEmitOriginalQuals());
+        }
         final BQSRMode mode = WalkerManager.getWalkerAnnotation(walker, BQSRMode.class);
         return mode.ApplicationTime();
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 54907f9f2..da6e68697 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -58,7 +58,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
-import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
+import org.broadinstitute.sting.utils.recalibration.BQSRArgumentSet;
 import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor;
 
 import java.io.File;
@@ -209,11 +209,11 @@ public class GenomeAnalysisEngine {
     /**
      *  Base Quality Score Recalibration helper object
      */
-    private BaseRecalibration baseRecalibration = null;
-    public BaseRecalibration getBaseRecalibration() { return baseRecalibration; }
-    public boolean hasBaseRecalibration() { return baseRecalibration != null; }
-    public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean emitOriginalQuals) {
-        baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan, emitOriginalQuals);
+    private BQSRArgumentSet bqsrArgumentSet = null;
+    public BQSRArgumentSet getBQSRArgumentSet() { return bqsrArgumentSet; }
+    public boolean hasBQSRArgumentSet() { return bqsrArgumentSet != null; }
+    public void setBaseRecalibration(final GATKArgumentCollection args) {
+        bqsrArgumentSet = new BQSRArgumentSet(args);
     }
 
     /**
@@ -242,7 +242,7 @@ public class GenomeAnalysisEngine {
 
         // if the use specified an input BQSR recalibration table then enable on the fly recalibration
         if (args.BQSR_RECAL_FILE != null)
-            setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN, args.emitOriginalQuals);
+            setBaseRecalibration(args);
 
         // Determine how the threads should be divided between CPU vs. IO.
         determineThreadAllocation();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index d9c7c9008..3a3a3d705 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -284,15 +284,15 @@ public class GATKArgumentCollection {
     @Argument(fullName = "preserve_qscores_less_than", shortName = "preserveQ", doc = "Bases with quality scores less than this threshold won't be recalibrated (with -BQSR)", required = false)
     public int PRESERVE_QSCORES_LESS_THAN = QualityUtils.MIN_USABLE_Q_SCORE;
 
-    @Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false)
-    public byte defaultBaseQualities = -1;
-
     // --------------------------------------------------------------------------------------------------------------
     //
     // Other utility arguments
     //
     // --------------------------------------------------------------------------------------------------------------
 
+    @Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false)
+    public byte defaultBaseQualities = -1;
+
     @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false)
     public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java
new file mode 100644
index 000000000..fbd69c762
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.recalibration;
+
+import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
+
+import java.io.File;
+
+public class BQSRArgumentSet {
+    // declare public, STL-style for easier and more efficient access:
+    private File BQSR_RECAL_FILE;
+    private int quantizationLevels;
+    private boolean disableIndelQuals;
+    private boolean emitOriginalQuals;
+    private int PRESERVE_QSCORES_LESS_THAN;
+
+    public BQSRArgumentSet(final GATKArgumentCollection args) {
+        this.BQSR_RECAL_FILE = args.BQSR_RECAL_FILE;
+        this.quantizationLevels = args.quantizationLevels;
+        this.disableIndelQuals = args.disableIndelQuals;
+        this.emitOriginalQuals = args.emitOriginalQuals;
+        this.PRESERVE_QSCORES_LESS_THAN = args.PRESERVE_QSCORES_LESS_THAN;
+    }
+
+    public File getRecalFile() { return BQSR_RECAL_FILE; }
+
+    public int getQuantizationLevels() { return quantizationLevels; }
+
+    public boolean shouldDisableIndelQuals() { return disableIndelQuals; }
+
+    public boolean shouldEmitOriginalQuals() { return emitOriginalQuals; }
+
+    public int getPreserveQscoresLessThan() { return PRESERVE_QSCORES_LESS_THAN; }
+
+    public void setRecalFile(final File BQSR_RECAL_FILE) {
+        this.BQSR_RECAL_FILE = BQSR_RECAL_FILE;
+    }
+
+    public void setQuantizationLevels(final int quantizationLevels) {
+        this.quantizationLevels = quantizationLevels;
+    }
+
+    public void setDisableIndelQuals(final boolean disableIndelQuals) {
+        this.disableIndelQuals = disableIndelQuals;
+    }
+
+    public void setEmitOriginalQuals(final boolean emitOriginalQuals) {
+        this.emitOriginalQuals = emitOriginalQuals;
+    }
+
+    public void setPreserveQscoresLessThan(final int PRESERVE_QSCORES_LESS_THAN) {
+        this.PRESERVE_QSCORES_LESS_THAN = PRESERVE_QSCORES_LESS_THAN;
+    }
+}