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 1a7900a6c..d7174536e 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
@@ -112,8 +112,11 @@ 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 only this many alleles will be used.  Note that genotyping sites with many alternate alleles is both CPU and memory intensive.
+     * then only this many alleles will be used.  Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
+     * scales exponentially based on the number of alternate alleles.  Unless there is a good reason to change the default value, we highly recommend
+     * that you not play around with this parameter.
      */
+    @Advanced
     @Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
     public int MAX_ALTERNATE_ALLELES = 3;
 
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 45d509cf8..038414522 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
@@ -39,6 +39,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
@@ -214,6 +216,10 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
      *
      **/
     public void initialize() {
+        // check for a bad max alleles value
+        if ( UAC.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED )
+            throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALLELES_THAT_CAN_BE_GENOTYPED);
+
         // warn the user for misusing EMIT_ALL_SITES
         if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES &&
                 UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY &&
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index 0dec305d2..2c4c4f607 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -210,7 +210,12 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
         final List<Allele> alleles = parseAlleles(ref, alts, lineNo);
 
         // find out our location
-        final int start = Integer.valueOf(locParts[1]);
+        int start = 0;
+        try {
+            start = Integer.valueOf(locParts[1]);
+        } catch (Exception e) {
+            generateException("the value in the POS field must be an integer but it was " + locParts[1], lineNo);
+        }
         int stop = start;
 
         // ref alleles don't need to be single bases for monomorphic sites