diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java b/archive/java/src/org/broadinstitute/sting/multisamplecaller/EMGenotypeCalculationModel.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java
rename to archive/java/src/org/broadinstitute/sting/multisamplecaller/EMGenotypeCalculationModel.java
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PointEstimateGenotypeCalculationModel.java b/archive/java/src/org/broadinstitute/sting/multisamplecaller/PointEstimateGenotypeCalculationModel.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PointEstimateGenotypeCalculationModel.java
rename to archive/java/src/org/broadinstitute/sting/multisamplecaller/PointEstimateGenotypeCalculationModel.java
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
index 2e352c79f..30d2d1c3c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
@@ -18,7 +18,6 @@ import java.util.*;
 public abstract class GenotypeCalculationModel implements Cloneable {
 
     public enum Model {
-        EM_POINT_ESTIMATE,
         JOINT_ESTIMATE,
         POOLED
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
index 5713a7c13..e97af33ad 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
@@ -64,9 +64,6 @@ public class GenotypeCalculationModelFactory {
                                                                    PrintStream beagleWriter) {
         GenotypeCalculationModel gcm;
         switch ( UAC.genotypeModel ) {
-            case EM_POINT_ESTIMATE:
-                gcm = new PointEstimateGenotypeCalculationModel();
-                break;
             case JOINT_ESTIMATE:
                 gcm = new DiploidGenotypeCalculationModel();
                 break;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 6d634b715..93ee147af 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -31,7 +31,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 public class UnifiedArgumentCollection {
 
     // control the various models to be used
-    @Argument(fullName = "genotype_model", shortName = "gm", doc = "Genotype calculation model to employ -- JOINT_ESTIMATE is currently the default, while POOLED and EM_POINT_ESTIMATE are available.", required = false)
+    @Argument(fullName = "genotype_model", shortName = "gm", doc = "Genotype calculation model to employ -- JOINT_ESTIMATE is currently the default, while POOLED is also available.", required = false)
     public GenotypeCalculationModel.Model genotypeModel = GenotypeCalculationModel.Model.JOINT_ESTIMATE;
 
     @Argument(fullName = "base_model", shortName = "bm", doc = "Base substitution model to employ -- EMPIRICAL is the recommended default, but it's possible to select the ONE_STATE and THREE_STATE models for comparison purposes", required = false)
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 52c60489a..dd5bca9f5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -97,7 +97,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      * @return UG calculation arguments object
      **/
     public static UGCalculationArguments getUnifiedCalculationArguments(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
-        return getUnifiedCalculationArguments(toolkit, UAC, null, null);
+        return getUnifiedCalculationArguments(toolkit, UAC, null);
     }
 
     /**
@@ -106,11 +106,10 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      * @param toolkit      the GATK Engine
      * @param UAC          the UnifiedArgumentCollection
      * @param writer       the genotype writer
-     * @param beagleWriter the beagle writer
      * @return UG calculation arguments object
      *
      **/
-    private static UGCalculationArguments getUnifiedCalculationArguments(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, GenotypeWriter writer, PrintStream beagleWriter) {
+    private static UGCalculationArguments getUnifiedCalculationArguments(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, GenotypeWriter writer) {
         UGCalculationArguments UG_args = new UGCalculationArguments();
         UG_args.UAC = UAC;
 
@@ -121,9 +120,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         if ( UAC.POOLSIZE < 1 && UAC.genotypeModel == GenotypeCalculationModel.Model.POOLED ) {
             throw new IllegalArgumentException("Attempting to use the POOLED model with a pool size less than 1. Please set the pool size to an appropriate value.");
         }
-        if ( beagleWriter != null && UAC.genotypeModel == GenotypeCalculationModel.Model.EM_POINT_ESTIMATE ) {
-            throw new IllegalArgumentException("BEAGLE output is not currently supported in the EM_POINT_ESTIMATE calculation model.");
-        }
         if ( toolkit.getArguments().numberOfThreads > 1 && UAC.ASSUME_SINGLE_SAMPLE != null ) {
             // the ASSUME_SINGLE_SAMPLE argument can't be handled (at least for now) while we are multi-threaded because the IO system doesn't know how to get the sample name
             throw new IllegalArgumentException("For technical reasons, the ASSUME_SINGLE_SAMPLE argument cannot be used with multiple threads");
@@ -257,19 +253,17 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      **/
     public void initialize() {
 
-        UG_args = getUnifiedCalculationArguments(getToolkit(), UAC, writer, beagleWriter);
+        UG_args = getUnifiedCalculationArguments(getToolkit(), UAC, writer);
 
         // initialize the writers
         if ( verboseWriter != null ) {
-            if ( UAC.genotypeModel != GenotypeCalculationModel.Model.EM_POINT_ESTIMATE ) {
-                StringBuilder header = new StringBuilder("AFINFO\tLOC\tMAF\tF\tNullAFpriors\t");
-                for ( char altAllele : BaseUtils.BASES ) {
-                    char base = Character.toUpperCase(altAllele);
-                    header.append("POfDGivenAFFor" + base + "\t");
-                    header.append("PosteriorAFFor" + base + "\t");
-                }
-                verboseWriter.println(header);
+            StringBuilder header = new StringBuilder("AFINFO\tLOC\tMAF\tF\tNullAFpriors\t");
+            for ( char altAllele : BaseUtils.BASES ) {
+                char base = Character.toUpperCase(altAllele);
+                header.append("POfDGivenAFFor" + base + "\t");
+                header.append("PosteriorAFFor" + base + "\t");
             }
+            verboseWriter.println(header);
         }
         if ( beagleWriter != null ) {
             beagleWriter.print("marker alleleA alleleB");
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java
index ed589ef4c..838bb47cf 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java
@@ -39,7 +39,6 @@ public class FindContaminatingReadGroupsWalker extends LocusWalker<Integer, Inte
 
     public void initialize() {
         UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
-        uac.genotypeModel = GenotypeCalculationModel.Model.EM_POINT_ESTIMATE;
         uac.CONFIDENCE_THRESHOLD = 50;
         ug = UnifiedGenotyper.getUnifiedCalculationArguments(getToolkit(), uac);
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java
index 10b6fa2df..9bdd63b34 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java
@@ -31,7 +31,6 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
 
     public void initialize() {
         UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
-        uac.genotypeModel = GenotypeCalculationModel.Model.EM_POINT_ESTIMATE;
         uac.CONFIDENCE_THRESHOLD = 50;
         uac.ALL_BASES = true;
         ug = UnifiedGenotyper.getUnifiedCalculationArguments(getToolkit(), uac);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 0d9cb3b95..f0405110c 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -13,27 +13,6 @@ import java.util.Map;
 
 public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // testing point estimate model
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    @Test
-    public void testMultiSamplePilot1PointEM() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("5ad3f97c886a3381821366caa9162c12"));
-        executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
-    }
-
-    @Test
-    public void testMultiSamplePilot2PointEM() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("73c80566c8353958b2ac61932f0b3812"));
-        executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
-    }
-
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing pooled model