diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index f9997bfd8..1b4703e4a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -190,11 +190,21 @@ public class SampleUtils {
 
     }
 
-    public static List<String> getSamplesFromCommandLineInput(Collection<String> sampleArgs) {
+    /**
+     * Returns a new set of samples, containing a final list of samples expanded from sampleArgs
+     *
+     * Each element E of sampleArgs can either be a literal sample name or a file.  For each E,
+     * we try to read a file named E from disk, and if possible all lines from that file are expanded
+     * into unique sample names.
+     *
+     * @param sampleArgs
+     * @return
+     */
+    public static Set<String> getSamplesFromCommandLineInput(Collection<String> sampleArgs) {
         if (sampleArgs != null) {
             // Let's first go through the list and see if we were given any files.  We'll add every entry in the file to our
             // sample list set, and treat the entries as if they had been specified on the command line.
-            List<String> samplesFromFiles = new ArrayList<String>();
+            Set<String> samplesFromFiles = new HashSet<String>();
             for (String SAMPLE_EXPRESSION : sampleArgs) {
                 File sampleFile = new File(SAMPLE_EXPRESSION);
 
@@ -203,7 +213,7 @@ public class SampleUtils {
 
                     List<String> lines = reader.readLines();
                     for (String line : lines) {
-                        samplesFromFiles.add(line);
+                        samplesFromFiles.add(line.trim());
                     }
                 } catch (FileNotFoundException e) {
                     samplesFromFiles.add(SAMPLE_EXPRESSION); // not a file, so must be a sample
@@ -212,7 +222,8 @@ public class SampleUtils {
 
             return samplesFromFiles;
         }
-        return new ArrayList<String>();
+
+        return new HashSet<String>();
     }
 
     public static Set<String> getSamplesFromCommandLineInput(Collection<String> vcfSamples, Collection<String> sampleExpressions) {