diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
index 9e1be5bca..976889613 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
@@ -369,9 +369,9 @@ public abstract class CommandLineProgram {
         System.exit(1);
     }
 
-    public static void exitSystemWithSamError(final Exception e) {
-        if ( e.getMessage() == null )
-            throw new ReviewedStingException("SamException found with no message!", e);
+    public static void exitSystemWithSamError(final Throwable t) {
+        if ( t.getMessage() == null )
+            throw new ReviewedStingException("SamException found with no message!", t);
 
         errorPrintf("------------------------------------------------------------------------------------------%n");
         errorPrintf("A BAM ERROR has occurred (version %s): %n", CommandLineGATK.getVersionNumber());
@@ -383,7 +383,7 @@ public abstract class CommandLineProgram {
         errorPrintf("Also, please ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n");
         printDocumentationReference();
         errorPrintf("%n");
-        errorPrintf("MESSAGE: %s%n", e.getMessage().trim());
+        errorPrintf("MESSAGE: %s%n", t.getMessage().trim());
         errorPrintf("------------------------------------------------------------------------------------------%n");
         System.exit(1);
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 70c6bc734..bc4c181be 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -101,20 +101,28 @@ public class CommandLineGATK extends CommandLineExecutable {
             // TODO: Should Picard exceptions be, in general, UserExceptions or ReviewedStingExceptions?
             exitSystemWithError(e);
         } catch (SAMException e) {
-            checkForTooManyOpenFilesProblem(e.getMessage());
+            checkForMaskedUserErrors(e);
             exitSystemWithSamError(e);
         } catch (OutOfMemoryError e) {
             exitSystemWithUserError(new UserException.NotEnoughMemory());
         } catch (Throwable t) {
-            checkForTooManyOpenFilesProblem(t.getMessage());
+            checkForMaskedUserErrors(t);
             exitSystemWithError(t);
         }
     }
 
-    private static void checkForTooManyOpenFilesProblem(String message) {
-        // Special case the "Too many open files" error because it's a common User Error for which we know what to do
-        if ( message != null && message.indexOf("Too many open files") != -1 )
+    private static void checkForMaskedUserErrors(final Throwable t) {
+        final String message = t.getMessage();
+        if ( message == null )
+            return;
+
+        // we know what to do about the common "Too many open files" error
+        if ( message.indexOf("Too many open files") != -1 )
             exitSystemWithUserError(new UserException.TooManyOpenFiles());
+
+        // Malformed BAM looks like a SAM file
+        if ( message.indexOf("Cannot use index file with textual SAM file") != -1 )
+            exitSystemWithSamError(t);
     }
 
     /**