diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
index 667ed47a1..116803ed6 100644
--- a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
@@ -22,7 +22,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
      * The supporting BWT index generated using BWT. 
      */
     @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
-    String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta";
+    private String prefix = null;
 
     /**
      * The instance used to generate alignments.
@@ -34,6 +34,8 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
      */
     @Override
     public void initialize() {
+        if(prefix == null)
+            prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();
         BWTFiles bwtFiles = new BWTFiles(prefix);
         BWAConfiguration configuration = new BWAConfiguration();
         aligner = new BWACAligner(bwtFiles,configuration);
diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
index 6127c7ac9..8fb2f5061 100644
--- a/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
@@ -20,13 +20,13 @@ import java.io.File;
 @WalkerName("Align")
 public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
-    String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta";
+    private String prefix = null;
 
     @Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
-    String outputBamFile = null;
+    private String outputBamFile = null;
 
     @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
-    Integer bamCompression = 5;
+    private Integer bamCompression = 5;
 
     /**
      * The actual aligner.
@@ -56,6 +56,8 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
      */    
     @Override
     public void initialize() {
+        if(prefix == null)
+            prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();        
         BWTFiles bwtFiles = new BWTFiles(prefix);
         BWAConfiguration configuration = new BWAConfiguration();
         aligner = new BWACAligner(bwtFiles,configuration);
diff --git a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
index 3fdd46952..30d892d71 100644
--- a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
@@ -20,7 +20,7 @@ public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
      * The supporting BWT index generated using BWT.
      */
     @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
-    String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta";
+    private String prefix = null;
 
     /**
      * The actual aligner.
@@ -34,6 +34,8 @@ public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
      */
     @Override
     public void initialize() {
+        if(prefix == null)
+            prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();        
         BWTFiles bwtFiles = new BWTFiles(prefix);
         BWAConfiguration configuration = new BWAConfiguration();
         aligner = new BWACAligner(bwtFiles,configuration);