diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
index 680f0b4e4..d54efee0f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
@@ -192,6 +192,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             String markerKey = phasedLine[1];
 
             HashMap<String,HaplotypePair> haplotypePairs = new HashMap<String,HaplotypePair>();
+            System.out.println(markerKey);
 
             j = 2;
             for (String sample : samples) {
@@ -235,30 +236,8 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
         return allThere;
 
     }
- /*
 
 
-    private class MyFileReader {
-        private FileReader reader;
-        private String fileName;
-        public MyFileReader(String fileName) {
-            try{
-                reader = new FileReader(fileName);
-            } catch ( FileNotFoundException e) {
-                throw new StingException("Could not find required input file: " + fileName);
-            }
-
-            this.fileName = fileName;
-
-        }
-        public String GetNextLine() {
-            String line;
-            int x = reader.read();
-            line.
-            //reader.read()
-        }
-    }     */
-    
     private class BeagleFileReader {
         private String headerString;
         private BufferedReader reader;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
index 4f13fa6c5..d83181963 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
@@ -90,9 +90,6 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
                 return 0;
             }
 
-             // Get Reference base for this site: will be output to screen, not directly used by Beagle but rather by output analysis tools
-       //     char re =  (char)ref.getBase();
-
             // output marker ID to Beagle input file
             beagleWriter.print(String.format("%s ",vc_eval.getLocation().toString()));
 
@@ -117,10 +114,21 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
                 if (genotype.isCalled() && genotype.hasAttribute(VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY)) {
                     String[] glArray = genotype.getAttributeAsString(VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY).split(",");
 
+                    Double maxLikelihood = -100.0;
+                    ArrayList<Double> likeArray = new ArrayList<Double>();
+
                     for (String gl : glArray) {
-                        Double d_gl = 100*Math.pow(10, Double.valueOf(gl));
-                        beagleWriter.print(String.format("%5.2f ",d_gl));
-                    }
+                        // need to normalize likelihoods to avoid precision loss. In worst case, if all 3 log-likelihoods are too
+                        // small, we could end up with linear likelihoods of form 0.00 0.00 0.00 which will mess up imputation.
+                        Double dg = Double.valueOf(gl);
+                        if (dg> maxLikelihood)
+                            maxLikelihood = dg;
+
+                        likeArray.add(dg);
+                     }
+
+                    for (Double likeVal: likeArray)
+                        beagleWriter.print(String.format("%5.4f ",Math.pow(10, likeVal-maxLikelihood)));
                 }
                 else
                     beagleWriter.print("0.33 0.33 0.33 "); // write 1/3 likelihoods for uncalled genotypes.