diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 4bea86161..f57c8873e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -74,7 +74,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
             bestAlternateAllele = alternateAlleleToUse.getBases()[0];
         } else if ( useAlleleFromVCF ) {
             final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
-            if ( vcInput == null || vcInput.isFiltered() )
+            if ( vcInput == null || vcInput.isFiltered() || !vcInput.isSNP() )
                 return null;
             if ( !vcInput.isSNP() ) {
                 logger.info("Record at position " + ref.getLocus() + " is not a SNP; skipping...");
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
index f3f48f501..4bfb93e80 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
@@ -47,7 +47,7 @@ import java.util.*;
  * the name 'allele' so we know which alternate allele to use at each site.
  */
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
-@Requires(value={},referenceMetaData=@RMD(name="allele", type= VariantContext.class))
+@Requires(value={},referenceMetaData=@RMD(name="alleles", type= VariantContext.class))
 @Reference(window=@Window(start=-200,stop=200))
 @By(DataSource.READS)
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
@@ -90,20 +90,7 @@ public class UGCalcLikelihoods extends LocusWalker<VariantCallContext, Integer>
     }
 
     public VariantCallContext map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
-        Collection<VariantContext> VCs = tracker.getVariantContexts(refContext, "allele", null, rawContext.getLocation(), true, false);
-        if ( VCs.size() == 0 )
-            return null;
-        if ( VCs.size() > 1 ) {
-            logger.warn("Multiple records seen in the 'allele' ROD at position " + rawContext.getLocation() + "; skipping...");
-            return null;
-        }
-        VariantContext vc = VCs.iterator().next();
-        if ( !vc.isBiallelic() ) {
-            logger.warn("The record in the 'allele' ROD at position " + rawContext.getLocation() + " is not biallelic; skipping...");
-            return null;
-        }
-
-        VariantContext call = UG_engine.calculateLikelihoods(tracker, refContext, rawContext, vc.getAlternateAllele(0), true);
+        VariantContext call = UG_engine.calculateLikelihoods(tracker, refContext, rawContext);
         return call == null ? null : new VariantCallContext(call, refContext.getBase(), true);
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index b3ff6af80..0cb942ab3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -139,12 +139,6 @@ public class UnifiedGenotyperEngine {
         if ( UAC.COVERAGE_AT_WHICH_TO_ABORT > 0 && rawContext.size() > UAC.COVERAGE_AT_WHICH_TO_ABORT )
             return null;
 
-        // special case handling - avoid extended event pileups when calling indels if we're genotyping given alleles
-        // TODO - is this the right solution? otherwise we trigger twice and we get duplicate entries
- /*       if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.DINDEL && rawContext.hasExtendedEventPileup()
-                && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES)
-            return null;
-   */
         final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel( rawContext );
         if( model == null ) {
             return null;
@@ -169,11 +163,9 @@ public class UnifiedGenotyperEngine {
      * @param tracker    the meta data tracker
      * @param refContext the reference base
      * @param rawContext contextual information around the locus
-     * @param alternateAlleleToUse the alternate allele to use, null if not set
-     * @param useBAQedPileup should we use the BAQed pileup?
      * @return the VariantContext object
      */
-    public VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext, Allele alternateAlleleToUse, boolean useBAQedPileup) {
+    public VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
         final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel( rawContext );
         if( model == null )
             return null;
@@ -182,7 +174,7 @@ public class UnifiedGenotyperEngine {
         if ( stratifiedContexts == null )
             return null;
 
-        return calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, alternateAlleleToUse, useBAQedPileup, model);
+        return calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
     }
 
     // private method called by both UnifiedGenotyper and UGCalcLikelihoods entry points into the engine