diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 899194cef..bf0084fd0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -30,15 +30,13 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.SortingVCFWriter;
-import org.broad.tribble.TribbleException;
+import org.broad.tribble.vcf.StandardVCFWriter;
 
 import java.io.File;
 import java.util.*;
@@ -56,7 +54,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
     @Output(doc="File to which variants should be written",required=true)
     protected File file = null;
-    protected SortingVCFWriter writer = null;
+    protected StandardVCFWriter writer = null;
 
     @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
     protected File CHAIN = null;
@@ -64,9 +62,6 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true)
     protected File NEW_SEQ_DICT = null;
 
-    @Argument(fullName="maxCachingDistance", shortName="cache", doc="Maximum genomic distance for which we will cache variants", required=false)
-    protected Integer maxCachingDistance = 50000;
-
     private LiftOver liftOver;
 
     private long successfulIntervals = 0, failedIntervals = 0;
@@ -82,8 +77,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));
 
         final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey("variant") ? vcfHeaders.get("variant").getMetaData() : null, samples);
-
-        writer = new SortingVCFWriter(file, maxCachingDistance);
+        writer = new StandardVCFWriter(file, false);
         writer.writeHeader(vcfHeader);
     }
 
@@ -95,11 +89,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
         if ( toInterval != null ) {
             vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length));
-            try {
-                writer.add(vc, ref.getBase());
-            } catch (TribbleException e) {
-                throw new UserException(e.getMessage());
-            }
+            writer.add(vc, ref.getBase());
             successfulIntervals++;
         } else {
             failedIntervals++;
@@ -122,8 +112,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
     public Integer reduce(Integer value, Integer sum) { return 0; }
 
     public void onTraversalDone(Integer result) {
-        writer.flush();
-        writer.close();
         System.out.println("Converted " + successfulIntervals + " records; failed to convert " + failedIntervals + " records.");
+        writer.close();
     }
 }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
index 785763dbd..2cd588003 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
@@ -49,7 +49,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + hg18Reference + " -B:variant,vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("ce71a6d40f7375826e31adb3832d2fe3"));
+                 Arrays.asList("22d4cd78d72da55f2423b9ab06f467b2"));
          executeTest("test hg18 to hg19, unsorted", spec);
     }
 }
\ No newline at end of file
diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl
index 4b3627612..e02ba98a8 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -11,7 +11,6 @@ my $chain = undef;
 my $newRef = undef;
 my $oldRef = undef;
 my $out = undef;
-my $cacheSize = 50000;
 my $tmp = "/tmp";
 GetOptions( "vcf=s" => \$in,
 	    "gatk=s" => \$gatk,
@@ -19,12 +18,11 @@ GetOptions( "vcf=s" => \$in,
 	    "newRef=s" => \$newRef,
 	    "oldRef=s" => \$oldRef,
             "out=s" => \$out,
-	    "cache=s" => \$cacheSize,
 	    "tmp=s" => \$tmp);
 
 if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out ) {
-    print "Usage: liftOverVCF.pl\n\t-vcf \t\t<input vcf>\n\t-gatk \t\t<path to gatk trunk>\n\t-chain \t\t<chain file>\n\t-newRef \t<path to new reference prefix; we will need newRef.dict, .fasta, and .fasta.fai>\n\t-oldRef \t<path to old reference prefix; we will need oldRef.fasta>\n\t-out \t\t<output vcf>\n\t-cache \t\t<cache size used for on-the-fly sorting; defaults to 50000>\n\t-tmp \t\t<temp file location; defaults to /tmp>\n";
-    print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /humgen/1kg/reference/human_b36_both\n\t-cache 60000\n";
+    print "Usage: liftOverVCF.pl\n\t-vcf \t\t<input vcf>\n\t-gatk \t\t<path to gatk trunk>\n\t-chain \t\t<chain file>\n\t-newRef \t<path to new reference prefix; we will need newRef.dict, .fasta, and .fasta.fai>\n\t-oldRef \t<path to old reference prefix; we will need oldRef.fasta>\n\t-out \t\t<output vcf>\n\t-tmp \t\t<temp file location; defaults to /tmp>\n";
+    print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /humgen/1kg/reference/human_b36_both\n";
     exit(1);
 }
 
@@ -32,19 +30,42 @@ if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out ) {
 my $random_number = rand();
 my $tmp_prefix = "$tmp/$random_number";
 print "Writing temporary files to prefix: $tmp_prefix\n";
-my $lifted_vcf = "$tmp_prefix.lifted.vcf";
+my $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
 
 # lift over the file
 print "Lifting over the vcf...";
-my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $lifted_vcf -chain $chain -dict $newRef.dict -cache $cacheSize";
+my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -B:variant,vcf $in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
 system($cmd);
 
+# we need to sort the lifted over file now
+print "\nRe-sorting the vcf...\n";
+my $sorted_vcf = "$tmp_prefix.sorted.vcf";
+open(SORTED, ">$sorted_vcf") or die "can't open $sorted_vcf: $!";
+
+# write the header
+open(UNSORTED, "< $unsorted_vcf") or die "can't open $unsorted_vcf: $!";
+my $inHeader = 1;
+while ( $inHeader == 1 ) {
+    my $line = <UNSORTED>;
+    if ( $line !~ m/^#/ ) {
+	$inHeader = 0;
+    } else {
+	print SORTED "$line";
+    }
+}
+close(UNSORTED);
+
+$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai";
+print SORTED `$cmd`;
+close(SORTED);
+
 # Filter the VCF for bad records
 print "\nFixing/removing bad records...\n";
-$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $lifted_vcf -o $out";
+$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $sorted_vcf -o $out";
 system($cmd);
 
 # clean up
-unlink $lifted_vcf;
+unlink $unsorted_vcf;
+unlink $sorted_vcf;
 
 print "\nDone!\n";