diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 2f8e7f40a..4db6f3611 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.utils;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -314,7 +315,7 @@ public class GenomeLocParser {
      * 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
      *
      * @param file_name
-     * @param rule also merge abutting intervals
+     * @return List<GenomeLoc> List of Genome Locs that have been parsed from file
      */
     public static List<GenomeLoc> intervalFileToList(final String file_name) {
         // try to open file
@@ -368,22 +369,15 @@ public class GenomeLocParser {
                 List<GenomeLoc> ret = new ArrayList<GenomeLoc>();
                 XReadLines reader = new XReadLines(new File(file_name));
                 for(String line: reader) {
-                    try {
                         ret.add(parseGenomeInterval(line));
-                    }
-                    catch (Exception e2) {
-                        throw new StingException(String.format("Unable to parse interval: %s in file: %s", line, file_name));
-                    }
                 }
                 reader.close();
 
                 // always return null instead of empty list
                 return ret.isEmpty() ? null : ret;
             }
-            catch (Exception e2) {
-                logger.error("Attempt to parse interval file in GATK format failed: " + e2.getMessage());
-                e2.printStackTrace();
-                throw new StingException("Unable to parse out interval file in either format", e);
+            catch (IOException e2) {
+                throw new StingException("An I/O error occurred while reading the interval file.", e);
             }
         }
     }
diff --git a/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index 73139d8ea..01396c4a8 100644
--- a/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -47,8 +47,16 @@ public class IntervalUtils {
                 for (String fileOrInterval : argument.split(";")) {
 
                     // if it's a file, add items to raw interval list
-                    if (isIntervalFile(fileOrInterval))
-                        rawIntervals.addAll(GenomeLocParser.intervalFileToList(fileOrInterval));
+                    if (isIntervalFile(fileOrInterval)) {
+                        try {
+                            rawIntervals.addAll(GenomeLocParser.intervalFileToList(fileOrInterval));
+                        }
+                        catch (Exception e) {
+                            throw new StingException(String.format("Interval file %s could not be parsed in either format. " +
+                                    "The problem is:%n%s",
+                                    fileOrInterval, e.getMessage()), e);
+                        }
+                    }
 
                         // otherwise treat as an interval -> parse and add to raw interval list
                     else {
@@ -88,15 +96,21 @@ public class IntervalUtils {
     public static boolean isIntervalFile(String str) {
         // should we define list of file extensions as a public array somewhere?
         // is regex or endsiwth better?
+        File file = new File(str);
         if (str.toUpperCase().endsWith(".BED") || str.toUpperCase().endsWith(".LIST") ||
                 str.toUpperCase().endsWith(".PICARD") || str.toUpperCase().endsWith(".INTERVAL_LIST")
-                || str.toUpperCase().endsWith(".INTERVALS"))
-            return true;
+                || str.toUpperCase().endsWith(".INTERVALS")) {
+            if (file.exists())
+                return true;
+            else
+                throw new StingException(String.format("The interval file %s does not exist.", file.getAbsolutePath()));
+        }
 
-        if(new File(str).exists())
-            throw new StingException("Interval argument looks like a filename, but does not have one of " +
-                                     "the supported extensions (.bed, .list, .picard, .interval_list, or .intervals).  " +
-                                     "Please rename your file with the appropriate extension.");
+        if(file.exists())
+            throw new StingException(String.format("The interval file %s does not have one of " +
+                    "the supported extensions (.bed, .list, .picard, .interval_list, or .intervals). " +
+                    "Please rename your file with the appropriate extension. If %s is NOT supposed to be a file, " +
+                    "please move or rename the file at location %s", str, str, file.getAbsolutePath()));
 
         else return false;
     }