diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index c4f1a286d..f01e8ad62 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -530,8 +530,8 @@ public class GenomeAnalysisEngine {
         }
 
         if ( duplicateSamFiles.size() > 0 ) {
-            throw new ArgumentException("The following BAM files appear multiple times in the list of input files: " +
-                                        duplicateSamFiles + " BAM files may be specified at most once.");
+            throw new UserException("The following BAM files appear multiple times in the list of input files: " +
+                                    duplicateSamFiles + " BAM files may be specified at most once.");
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
index 7efab5fb0..72c037707 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
@@ -98,7 +98,7 @@ public class SAMReaderID implements Comparable {
         if(!(other instanceof SAMReaderID)) return false;
 
         SAMReaderID otherID = (SAMReaderID)other;
-        return this.samFile.equals(otherID.samFile);
+        return this.getSamFilePath().equals(otherID.getSamFilePath());
     }
 
     /**
@@ -107,7 +107,7 @@ public class SAMReaderID implements Comparable {
      */
     @Override
     public int hashCode() {
-        return samFile.hashCode();
+        return samFile.getAbsolutePath().hashCode();
     }
 
     /**
diff --git a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
index 3f74e0eae..c3bc78551 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
@@ -52,7 +52,7 @@ import java.util.List;
  */
 public class GenomeAnalysisEngineUnitTest extends BaseTest {
 
-    @Test(expectedExceptions=ArgumentException.class)
+    @Test(expectedExceptions=UserException.class)
     public void testDuplicateSamFileHandlingSingleDuplicate() throws Exception {
         GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
 
@@ -64,7 +64,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         testEngine.checkForDuplicateSamFiles();
     }
 
-    @Test(expectedExceptions=ArgumentException.class)
+    @Test(expectedExceptions=UserException.class)
     public void testDuplicateSamFileHandlingMultipleDuplicates() throws Exception {
         GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
 
@@ -78,6 +78,20 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         testEngine.checkForDuplicateSamFiles();
     }
 
+    @Test(expectedExceptions=UserException.class)
+    public void testDuplicateSamFileHandlingAbsoluteVsRelativePath() {
+        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
+
+        final File relativePathToBAMFile = new File("public/testdata/exampleBAM.bam");
+        final File absolutePathToBAMFile = new File(relativePathToBAMFile.getAbsolutePath());
+        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
+        samFiles.add(new SAMReaderID(relativePathToBAMFile, new Tags()));
+        samFiles.add(new SAMReaderID(absolutePathToBAMFile, new Tags()));
+
+        testEngine.setSAMFileIDs(samFiles);
+        testEngine.checkForDuplicateSamFiles();
+    }
+
     @Test
     public void testEmptyIntervalSetHandling() throws Exception {
         GenomeLocParser genomeLocParser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000).getSequenceDictionary());
diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java
new file mode 100644
index 000000000..a594573e5
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java
@@ -0,0 +1,49 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.gatk.datasources.reads;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.commandline.Tags;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+
+public class SAMReaderIDUnitTest extends BaseTest {
+
+    @Test
+    public void testSAMReaderIDHashingAndEquality() {
+        // Test to make sure that two SAMReaderIDs that point at the same file via an absolute vs. relative
+        // path are equal according to equals() and have the same hash code
+        final File relativePathToBAMFile = new File("public/testdata/exampleBAM.bam");
+        final File absolutePathToBAMFile = new File(relativePathToBAMFile.getAbsolutePath());
+        final SAMReaderID relativePathSAMReaderID = new SAMReaderID(relativePathToBAMFile, new Tags());
+        final SAMReaderID absolutePathSAMReaderID = new SAMReaderID(absolutePathToBAMFile, new Tags());
+
+        Assert.assertEquals(relativePathSAMReaderID, absolutePathSAMReaderID, "Absolute-path and relative-path SAMReaderIDs not equal according to equals()");
+        Assert.assertEquals(relativePathSAMReaderID.hashCode(), absolutePathSAMReaderID.hashCode(), "Absolute-path and relative-path SAMReaderIDs have different hash codes");
+    }
+}