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 01344a117..710127f7a 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
@@ -7,6 +7,8 @@ import org.broad.tribble.NameAwareCodec;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -96,6 +98,9 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
         for ( String str : headerStrings ) {
             if ( !str.startsWith(VCFHeader.METADATA_INDICATOR) ) {
                 String[] strings = str.substring(1).split(VCFConstants.FIELD_SEPARATOR);
+                if ( strings.length < VCFHeader.HEADER_FIELDS.values().length )
+                    throw new TribbleException.InvalidHeader("there are not enough columns present in the header line: " + str);
+
                 int arrayIndex = 0;
                 for (VCFHeader.HEADER_FIELDS field : VCFHeader.HEADER_FIELDS.values()) {
                     try {
@@ -159,12 +164,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
     }
 
     private Feature reallyDecode(String line) {
-        try {
             // the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
             if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
 
             // our header cannot be null, we need the genotype sample names and counts
-            if (header == null) throw new IllegalStateException("VCF Header cannot be null when decoding a record");
+            if (header == null) throw new ReviewedStingException("VCF Header cannot be null when decoding a record");
 
             if (parts == null)
                 parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)];
@@ -174,17 +178,18 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
             // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.  Otherwise check that we have nine (normal colummns + genotyping data)
             if (( (header == null || (header != null && !header.hasGenotypingData())) && nParts != NUM_STANDARD_FIELDS) ||
                  (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
-                throw new IllegalArgumentException("There aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
-                        " tokens, and saw " + nParts + " )");
+                throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
+                        " tokens, and saw " + nParts + " )", lineNo);
 
             return parseVCFLine(parts);
-        } catch (TribbleException e) {
-            throw new TribbleException.InvalidDecodeLine(e.getMessage(), line);
-        }
     }
 
     protected void generateException(String message) {
-        throw new TribbleException.InvalidDecodeLine(message, lineNo);
+        throw new UserException.MalformedVCF(message, lineNo);
+    }
+
+    private static void generateException(String message, int lineNo) {
+        throw new UserException.MalformedVCF(message, lineNo);
     }
 
     /**
@@ -472,10 +477,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
         return true;
     }
 
-    private static void generateException(String message, int lineNo) {
-        throw new TribbleException.InvalidDecodeLine(message, lineNo);
-    }
-
     private static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
         boolean clipping = true;
         // Note that the computation of forward clipping here is meant only to see whether there is a common
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 0be4bec91..17c4a7df4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -154,6 +154,16 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class MalformedVCF extends UserException {
+        public MalformedVCF(String message, String line) {
+            super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
+        }
+
+        public MalformedVCF(String message, int lineNo) {
+            super(String.format("The provided VCF file is malformed at line nmber %d: %s", lineNo, message));
+        }
+    }
+
     public static class ReadMissingReadGroup extends MalformedBAM {
         public ReadMissingReadGroup(SAMRecord read) {
             super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName()));