diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsCalculationModel.java
index 8b5639817..37b676601 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypeLikelihoodsCalculationModel.java
@@ -213,7 +213,7 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi
         if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) {
             AlignmentContext mergedContext = AlignmentContextUtils.joinContexts(contexts.values());
             Map<String,AlignmentContext> newContext = new HashMap<String,AlignmentContext>();
-            newContext.put(DUMMY_POOL,mergedContext);
+            newContext.put(DUMMY_SAMPLE_NAME,mergedContext);
             contexts = newContext;
         }
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java
index 0922b8e7f..c2bac4455 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolIndelGenotypeLikelihoodsCalculationModel.java
@@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.variantcontext.*;
 import java.util.*;
 
 public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLikelihoodsCalculationModel {
+    private static final int MAX_NUM_ALLELES_TO_GENOTYPE = 4;
 
     private PairHMMIndelErrorModel pairModel;
     private boolean allelesArePadded = false;
@@ -94,7 +95,10 @@ public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLi
 
 
         final Pair<List<Allele>,Boolean> pair = IndelGenotypeLikelihoodsCalculationModel.getInitialAlleleList(tracker, ref, contexts, contextType, locParser, UAC,true);
-        final List<Allele> alleles = pair.first;
+        List<Allele> alleles = pair.first;
+
+        if (alleles.size() > MAX_NUM_ALLELES_TO_GENOTYPE)
+            alleles = alleles.subList(0,MAX_NUM_ALLELES_TO_GENOTYPE);
         allelesArePadded = pair.second;
         if (contextType == AlignmentContextUtils.ReadOrientation.COMPLETE) {
             IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap().clear();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
index 84467085b..4253ff3ad 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
@@ -48,7 +48,7 @@ import java.util.Map;
 public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
 
     public static final String DUMMY_LANE = "Lane1";
-    public static final String DUMMY_POOL = "Pool1";
+    public static final String DUMMY_SAMPLE_NAME = "DummySample1";
 
     /*    public enum Model {
           SNP,
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 31a2dfd77..d504badab 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -25,10 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.DownsampleType;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -40,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -226,7 +225,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
     public void initialize() {
 
         // Check for protected modes
-        if (getToolkit().isGATKLite()) {
+        if (GATKLiteUtils.isGATKLite()) {
             // no polyploid/pooled mode in GATK Like
             if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY ||
                     UAC.referenceSampleName != null ||
@@ -240,7 +239,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
             // in full mode: check for consistency in ploidy/pool calling arguments
             // check for correct calculation models
             if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) {
-                // polyploidy required POOL GL and AF calculation models to be specified right now
+                // polyploidy requires POOL GL and AF calculation models to be specified right now
                 if (UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLSNP && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLINDEL
                         && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLBOTH)   {
                     throw new UserException("Incorrect genotype calculation model chosen. Only [POOLSNP|POOLINDEL|POOLBOTH] supported with this walker if sample ploidy != 2");
@@ -253,7 +252,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
             // get all of the unique sample names
             if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) {
                 samples.clear();
-                samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_POOL);
+                samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME);
             } else {
                 samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
                 if (UAC.referenceSampleName != null )