diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
index 5ad213903..5345f9f48 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -45,8 +46,7 @@ public class DepthOfCoverageStats {
 
     public static int[] calculateBinEndpoints(int lower, int upper, int bins) {
         if ( bins > upper - lower || lower < 1 ) {
-            throw new IllegalArgumentException("Illegal argument to calculateBinEndpoints; "+
-                    "lower bound must be at least 1, and number of bins may not exceed stop - start");
+            throw new UserException.BadInput("the start must be at least 1 and the number of bins may not exceed stop - start");
         }
 
         int[] binLeftEndpoints = new int[bins+1];
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
index efcd3ecf0..cb392f29c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java
@@ -73,6 +73,8 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
         } catch ( UserException.MalformedGenomeLoc e ) {
             Utils.warnUser("RefSeq file is potentially incorrect, as some transcripts or exons have a negative length ("+fields[2]+")");
             return null;
+        } catch ( NumberFormatException e ) {
+            throw new UserException.MalformedFile("Could not parse location from line: " + line);
         }
     }
 
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 2c4c4f607..a1127e35d 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
@@ -473,7 +473,12 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
     protected static Allele oneAllele(String index, List<Allele> alleles) {
         if ( index.equals(VCFConstants.EMPTY_ALLELE) )
             return Allele.NO_CALL;
-        int i = Integer.valueOf(index);
+        final int i;
+        try {
+            i = Integer.valueOf(index);
+        } catch ( NumberFormatException e ) {
+            throw new TribbleException.InternalCodecException("The following invalid GT allele index was encountered in the file: " + index);
+        }
         if ( i >= alleles.size() )
             throw new TribbleException.InternalCodecException("The allele with index " + index + " is not defined in the REF/ALT columns in the record");
         return alleles.get(i);