diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
index 80618cfdb..d6cddcf84 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
@@ -56,7 +56,8 @@ public class AdvancedPerReadAlleleLikelihoodMap extends StandardPerReadAlleleLik
 
         for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
             final Allele bestAllele = getMostLikelyAllele(entry.getValue());
-            alleleReadMap.get(bestAllele).add(entry.getKey());
+            if ( bestAllele != Allele.NO_CALL )
+                alleleReadMap.get(bestAllele).add(entry.getKey());
         }
 
         // compute the reads to remove and actually remove them
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
index 36456ca09..2f6d9d16f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
@@ -79,7 +79,7 @@ public class StandardCallerArgumentCollection {
     public double CONTAMINATION_FRACTION = 0.0;
 
     @Hidden
-    @Argument(shortName = "logRemovedReadsFromContaminationFiltering", doc="contaminationLog", required=false)
+    @Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false)
     public PrintStream contaminationLog = null;
 
     @Hidden
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 3116d3a7d..a17c2aa1a 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
@@ -234,36 +234,21 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
             if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY ||
                     UAC.referenceSampleName != null ||
                     UAC.referenceSampleRod.isBound())  {
-                throw new UserException.NotSupportedInGATKLite("Usage of ploidy values different than 2 not supported in this GATK version");
+                throw new UserException.NotSupportedInGATKLite("you cannot enable usage of ploidy values other than 2");
             }
+
+            if ( UAC.CONTAMINATION_FRACTION > 0.0 ) {
+                throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling");
+            }
+        }
+
+        if ( UAC.TREAT_ALL_READS_AS_SINGLE_POOL ) {
+            samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME);
+        } else {
             // get all of the unique sample names
             samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
-
-        } else {
-            // in full mode: check for consistency in ploidy/pool calling arguments
-            // check for correct calculation models
-/*            if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) {
-                // 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");
-                }
-
-                if (UAC.AFmodel != AFCalc.Model.POOL)
-                    throw new UserException("Incorrect AF Calculation model. Only POOL model supported if sample ploidy != 2");
-
-            }
-  */
-            // get all of the unique sample names
-            if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) {
-                samples.clear();
-                samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME);
-            } else {
-                samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
-                if (UAC.referenceSampleName != null )
-                    samples.remove(UAC.referenceSampleName);
-            }
-
+            if ( UAC.referenceSampleName != null )
+                samples.remove(UAC.referenceSampleName);
         }
 
         // check for a bad max alleles value