diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
index 42bd8af9c..4232bdf92 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -485,6 +485,9 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         } else {
             printMappingsSorted(recalTableStream, 0, new Object[requestedCovariates.size()], dataManager.data.data);
         }
+
+        // print out an EOF marker
+        recalTableStream.println(TableRecalibrationWalker.EOF_MARKER);
     }
 
     private void printMappingsSorted( final PrintStream recalTableStream, final int curPos, final Object[] key, final Map data) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 9d743d781..b95655c18 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -53,7 +53,6 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
@@ -104,6 +103,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     /////////////////////////////
     @Argument(fullName="no_pg_tag", shortName="noPG", required=false, doc="Don't output the usual PG tag in the recalibrated bam file header. FOR DEBUGGING PURPOSES ONLY. This option is required in order to pass integration tests.")
     private boolean NO_PG_TAG = false;
+    @Argument(fullName="fail_with_no_eof_marker", shortName="requireEOF", required=false, doc="If no EOF marker is present in the covariates file, exit the program with an exception.")
+    private boolean REQUIRE_EOF = false;
 
     /////////////////////////////
     // Private Member Variables
@@ -113,6 +114,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
     private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
     private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
     private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
+    protected static final String EOF_MARKER = "EOF";
     private static final long RANDOM_SEED = 1032861495;
     private final Random coinFlip = new Random( RANDOM_SEED ); // Random number generator is used to remove reference bias in solid bams
     private long numReadsWithMalformedColorSpace = 0;
@@ -162,10 +164,13 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         // Read in the data from the csv file and populate the data map and covariates list
         logger.info( "Reading in the data from input csv file..." );
 
+        boolean sawEOF = false;
         try {
             for ( String line : new XReadLines(new File( RAC.RECAL_FILE )) ) {
                 lineNumber++;
-                if( COMMENT_PATTERN.matcher(line).matches() || OLD_RECALIBRATOR_HEADER.matcher(line).matches() )  {
+                if ( EOF_MARKER.equals(line) ) {
+                    sawEOF = true;
+                } else if( COMMENT_PATTERN.matcher(line).matches() || OLD_RECALIBRATOR_HEADER.matcher(line).matches() )  {
                     ; // Skip over the comment lines, (which start with '#')
                 }
                 // Read in the covariates that were used from the input file
@@ -227,6 +232,13 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         }
         logger.info( "...done!" );
 
+        if ( !sawEOF ) {
+            final String errorMessage = "No EOF marker was present in the recal covariates table; this could mean that the file is corrupted or was generated with an old version of the CountCovariates tool.";
+            if ( REQUIRE_EOF )
+                throw new StingException(errorMessage);
+            logger.warn(errorMessage);
+        }
+
         logger.info( "The covariates being used here: " );
         for( Covariate cov : requestedCovariates ) {
             logger.info( "\t" + cov.getClass().getSimpleName() );
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index e19d2fdb5..f375e6616 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -17,10 +17,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariates1() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7a23c3ffc3917f95117971d642bbeb56" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "89084b43b824f9e3c5e2afdfe0930542");
-        e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "7d6428a76e07ed4b99351aa4df89634d" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "a582a86adffee2c9ee79a00b424a6cd9" );
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "b2191ea11f528b9605b727d8a73dd1e1");
+        e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "596a9ec9cbc1da70481e45a5a588a41d" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "507dbd3ba6f54e066d04c4d24f59c3ab" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -81,7 +81,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesUseOriginalQuals() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "784488e7024f3e5398ca462d6b8f97c4");
+        e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "72b79646061d78674a3752272823d47f");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -135,7 +135,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesSolidIndelsRemoveRefBias() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "3889abcc7f6fe420f546fc049bfc2b5a" );
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "013822cfa4f276d48ca99c014c23c124" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -192,7 +192,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesVCF() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "9b9d21ffb70f15ef2aebad21f3fc05cb");
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "3700eaf567e4937f442fc777a226d6ad");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -216,7 +216,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesVCFPlusDBsnp() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "cc1cc9c1ff184d388d81574fdccc608e");
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "949c2ecb24a4189e106d372b05ec725f");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -244,7 +244,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesNoReadGroups() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "a86c64f649b847b7f81ac50a808d3d45" );
+        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "62dab3db2172695cf95fba7f543a4058" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -303,7 +303,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesNoIndex() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "481de3cbecad59c00cc148bbcd279e60" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "abc4248cb5f718594a63409a151d679e" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();