diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index bfa87122c..53600b145 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -159,7 +159,7 @@ public class UnifiedArgumentCollection {
 
     /**
      * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
-     * then this site will be skipped and a warning printed.
+     * then this site will be skipped and a warning printed.  Note that genotyping sites with many alternate alleles is both CPU and memory intensive.
      */
     @Hidden
     @Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 6a79061fc..6e61790ed 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -38,7 +38,6 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -153,8 +152,6 @@ public class UnifiedGenotyperEngine {
         }
         
         VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
-        VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
-
         if ( vc == null )
             return null;
 
@@ -297,13 +294,15 @@ public class UnifiedGenotyperEngine {
 
         // initialize the data for this thread if that hasn't been done yet
         if ( afcm.get() == null ) {
-            log10AlleleFrequencyPosteriors.set(new double[MAX_NUMBER_OF_ALTERNATE_ALLELES][N+1]);
+            log10AlleleFrequencyPosteriors.set(new double[UAC.MAX_ALTERNATE_ALLELES][N+1]);
             afcm.set(getAlleleFrequencyCalculationObject(N, logger, verboseWriter, UAC));
         }
 
         // don't try to genotype too many alternate alleles
-        if ( vc.getAlternateAlleles().size() > MAX_NUMBER_OF_ALTERNATE_ALLELES )
-            throw new UserException("the Unified Genotyper is currently not equipped to genotype more than " + MAX_NUMBER_OF_ALTERNATE_ALLELES + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + vc.getAlternateAlleles().size() + " alternate alleles");
+        if ( vc.getAlternateAlleles().size() > UAC.MAX_ALTERNATE_ALLELES ) {
+            logger.warn("the Unified Genotyper is currently set to genotype at most " + UAC.MAX_ALTERNATE_ALLELES + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + vc.getAlternateAlleles().size() + " alternate alleles; see the --max_alternate_alleles argument");
+            return null;
+        }
 
         // estimate our confidence in a reference call and return
         if ( vc.getNSamples() == 0 )
@@ -446,13 +445,15 @@ public class UnifiedGenotyperEngine {
 
         // initialize the data for this thread if that hasn't been done yet
         if ( afcm.get() == null ) {
-            log10AlleleFrequencyPosteriors.set(new double[MAX_NUMBER_OF_ALTERNATE_ALLELES][N+1]);
+            log10AlleleFrequencyPosteriors.set(new double[UAC.MAX_ALTERNATE_ALLELES][N+1]);
             afcm.set(getAlleleFrequencyCalculationObject(N, logger, verboseWriter, UAC));
         }
 
         // don't try to genotype too many alternate alleles
-        if ( vc.getAlternateAlleles().size() > MAX_NUMBER_OF_ALTERNATE_ALLELES )
-            throw new UserException("the Unified Genotyper is currently not equipped to genotype more than " + MAX_NUMBER_OF_ALTERNATE_ALLELES + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + vc.getAlternateAlleles().size() + " alternate alleles");
+        if ( vc.getAlternateAlleles().size() > UAC.MAX_ALTERNATE_ALLELES ) {
+            logger.warn("the Unified Genotyper is currently set to genotype at most " + UAC.MAX_ALTERNATE_ALLELES + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + vc.getAlternateAlleles().size() + " alternate alleles; see the --max_alternate_alleles argument");
+            return null;
+        }
 
         // estimate our confidence in a reference call and return
         if ( vc.getNSamples() == 0 )