diff --git a/java/src/org/broadinstitute/sting/gatk/ReadProperties.java b/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
index 3ac0ce429..b93b88152 100755
--- a/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
+++ b/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
@@ -6,7 +6,7 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
-import org.broadinstitute.sting.utils.BAQ;
+import org.broadinstitute.sting.utils.baq.BAQ;
 
 import java.util.List;
 import java.util.Collection;
diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 7de4c0154..6ee58b862 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -34,7 +34,7 @@ import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.gatk.DownsamplingMethod;
 import org.broadinstitute.sting.utils.interval.IntervalSetRule;
-import org.broadinstitute.sting.utils.BAQ;
+import org.broadinstitute.sting.utils.baq.BAQ;
 import org.simpleframework.xml.*;
 import org.simpleframework.xml.core.Persister;
 import org.simpleframework.xml.stream.Format;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
index c32c4661d..9b428f23f 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
@@ -44,7 +44,8 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.BAQ;
+import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.baq.BAQSamIterator;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java
index 7486eda1b..458a0097e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.BAQ;
+import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.Argument;
diff --git a/java/src/org/broadinstitute/sting/utils/BAQ.java b/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/BAQ.java
rename to java/src/org/broadinstitute/sting/utils/baq/BAQ.java
index 6d49ef291..86a9f7b08 100644
--- a/java/src/org/broadinstitute/sting/utils/BAQ.java
+++ b/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.utils.baq;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.CigarElement;
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BAQSamIterator.java b/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
similarity index 89%
rename from java/src/org/broadinstitute/sting/gatk/iterators/BAQSamIterator.java
rename to java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
index 4095cae20..7fff240f2 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/BAQSamIterator.java
+++ b/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
@@ -1,8 +1,9 @@
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.sting.utils.baq;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.BAQ;
+import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 
 import java.util.Iterator;
 
diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
index 64efe19b2..e61d6f836 100644
--- a/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
@@ -13,7 +13,7 @@ import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.BAQ;
+import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;