diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 235c13ada..6d7244043 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -371,14 +371,7 @@ public class GenomeAnalysisEngine {
         validateSuppliedReferenceAgainstWalker(my_walker, argCollection);
         referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile);
 
-        //
-        // please don't use these in the future, use the new syntax <- if we're not using these please remove them
-        //
         if (argCollection.DBSNPFile != null) bindConvenienceRods(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile);
-        if (argCollection.HAPMAPFile != null)
-            bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", argCollection.HAPMAPFile);
-        if (argCollection.HAPMAPChipFile != null)
-            bindConvenienceRods("hapmap-chip", "GFF", argCollection.HAPMAPChipFile);
         // TODO: The ROD iterator currently does not understand multiple intervals file.  Fix this by cleaning the ROD system.
         if (argCollection.intervals != null && argCollection.intervals.size() == 1) {
             bindConvenienceRods("interval", "Intervals", argCollection.intervals.get(0).replaceAll(",", ""));
diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 514844948..c3d8f8ef4 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -33,7 +33,6 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.gatk.DownsamplingMethod;
-import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import org.broadinstitute.sting.utils.interval.IntervalSetRule;
 import org.simpleframework.xml.*;
 import org.simpleframework.xml.core.Persister;
@@ -111,14 +110,6 @@ public class GATKArgumentCollection {
     @Input(fullName = "DBSNP", shortName = "D", doc = "DBSNP file", required = false)
     public String DBSNPFile = null;
 
-    @Element(required = false)
-    @Input(fullName = "hapmap", shortName = "H", doc = "Hapmap file", required = false)
-    public String HAPMAPFile = null;
-
-    @Element(required = false)
-    @Input(fullName = "hapmap_chip", shortName = "hc", doc = "Hapmap chip file", required = false)
-    public String HAPMAPChipFile = null;
-
     /**
      * The override mechanism in the GATK, by default, populates the command-line arguments, then
      * the defaults from the walker annotations.  Unfortunately, walker annotations should be trumped
@@ -315,12 +306,6 @@ public class GATKArgumentCollection {
         if (!other.DBSNPFile.equals(this.DBSNPFile)) {
             return false;
         }
-        if (!other.HAPMAPFile.equals(this.HAPMAPFile)) {
-            return false;
-        }
-        if (!other.HAPMAPChipFile.equals(this.HAPMAPChipFile)) {
-            return false;
-        }
         if (!other.unsafe.equals(this.unsafe)) {
             return false;
         }
diff --git a/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java b/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
index 7a5db4755..ff436ae44 100755
--- a/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.arguments;
 
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.junit.After;
 import static org.junit.Assert.fail;
 import org.junit.Before;
@@ -83,8 +82,6 @@ public class GATKArgumentCollectionUnitTest extends BaseTest {
         collect.strictnessLevel = SAMFileReader.ValidationStringency.STRICT;
         collect.referenceFile = new File("referenceFile".toLowerCase());
         collect.DBSNPFile = "DBSNPFile".toLowerCase();
-        collect.HAPMAPFile = "HAPMAPFile".toLowerCase();
-        collect.HAPMAPChipFile = "HAPMAPChipFile".toLowerCase();
         collect.unsafe = ValidationExclusion.TYPE.ALL;
         collect.downsampleFraction = null;
         collect.downsampleCoverage = null;
diff --git a/perl/runReleaseSanityCheck.pl b/perl/runReleaseSanityCheck.pl
index b559c139b..bc9edd194 100755
--- a/perl/runReleaseSanityCheck.pl
+++ b/perl/runReleaseSanityCheck.pl
@@ -31,23 +31,23 @@ $command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK
 run($command, $dry);
 
 print "Executing IndelRealignerWholeExome...";
-$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L chr1:900,000-1,000,000 -compress 1 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.realigner.intervals -O $tmp_bam";
+$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L chr1:900,000-1,000,000 -compress 1 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.realigner.intervals -o $tmp_bam";
 run($command, $dry);
 
 print "Executing IndelRealignerWholeGenome...";
-$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:975,000-1,000,000 -compress 1 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.realigner.intervals -O $tmp_bam";
+$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:975,000-1,000,000 -compress 1 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.realigner.intervals -o $tmp_bam";
 run($command, $dry);
 
 print "Executing UnifiedGenotyperWholeExome...";
-$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null -XL chr1:1,500,000-247179187";
+$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null -XL chr1:1,500,000-247179187";
 run($command, $dry);
 
 print "Executing UnifiedGenotyperWholeGenome...";
-$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:750,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null";
+$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:750,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null";
 run($command, $dry);
 
 print "Executing UnifiedGenotyperWholeGenomeMultithreaded...";
-$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:500,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null -nt 4";
+$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:500,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null -nt 4";
 run($command, $dry);
 
 unlink $tmp_bam;