diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index 0d64c9e18..898852211 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -254,7 +254,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
             if ( REF_FILE_ARG == null )
                 Utils.scareUser(String.format("Locus-based traversals require a reference file but none was given"));
 
-
             if ( INPUT_FILE == null ) {
                 if ( walker.requiresReads() )
                     Utils.scareUser(String.format("Analysis %s requires reads, but none were given", Analysis_Name));
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
index 11a9d7aed..9b33c789c 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
@@ -63,7 +63,8 @@ public class TraverseByReads extends TraversalEngine {
                 verifyingSamReadIter.setCheckOrderP(false);
         }
 
-        verifySortOrder(refFileName != null || walker.requiresOrderedReads());
+        if ( samReader != null )
+            verifySortOrder(refFileName != null || walker.requiresOrderedReads());
 
         // Initialize the walker
         walker.initialize();