diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
index 635a74399..1d506b88c 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
@@ -59,7 +59,7 @@ public class BQSRIntegrationTest extends WalkerTest {
     @Test(dataProvider = "BQSRTest")
     public void testBQSR(BQSRTest params) {
         WalkerTestSpec spec = new WalkerTestSpec(
-                " -T BQSR" +
+                " -T BaseRecalibrator" +
                         " -R " + params.reference +
                         " -I " + params.bam +
                         " -L " + params.interval +
@@ -74,7 +74,7 @@ public class BQSRIntegrationTest extends WalkerTest {
     @Test
     public void testBQSRFailWithoutDBSNP() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                " -T BQSR" +
+                " -T BaseRecalibrator" +
                         " -R " + b36KGReference +
                         " -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" +
                         " -L 1:10,000,000-10,200,000" +
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
index 1a03ce1ce..0b1f2c478 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
@@ -106,7 +106,7 @@ import java.util.ArrayList;
 @Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES})                                         // filter out all reads with zero or unavailable mapping quality
 @PartitionBy(PartitionType.LOCUS)                                                                                       // this walker requires both -I input.bam and -R reference.fasta
 
-public class BQSR extends LocusWalker<Long, Long> implements TreeReducible<Long> {
+public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long> {
     @ArgumentCollection
     private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();                          // all the command line arguments for BQSR and it's covariates
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
index 55c04f1b7..a24506d07 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
@@ -105,6 +105,6 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
      * @return the covariate keysets for this read
      */
     protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) {
-        return (ReadCovariates) read.getTemporaryAttribute(BQSR.COVARS_ATTRIBUTE);
+        return (ReadCovariates) read.getTemporaryAttribute(BaseRecalibrator.COVARS_ATTRIBUTE);
     }
 }
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index 70c89ac31..56e2ddebb 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -343,7 +343,7 @@ class DataProcessingPipeline extends QScript {
     this.jobName = queueLogDir + outBam + ".clean"
   }
 
-  case class cov (inBam: File, outRecalFile: File) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs {
+  case class cov (inBam: File, outRecalFile: File) extends BaseRecalibrator with CommandLineGATKArgs {
     this.knownSites ++= qscript.dbSNP
     this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
     this.input_file :+= inBam
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
index 86f2d4969..b7246ca8f 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
@@ -160,7 +160,7 @@ class PacbioProcessingPipeline extends QScript {
     this.jobName = queueLogDir + outBam + ".rg"
   }
 
-  case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs {
+  case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends BaseRecalibrator with CommandLineGATKArgs {
     if (resetQuals) 
       this.DBQ = dbq
     this.knownSites :+= dbSNP