diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl
index e02ba98a8..4b3627612 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -11,6 +11,7 @@ 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,
@@ -18,11 +19,12 @@ 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-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";
+    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";
     exit(1);
 }
 
@@ -30,42 +32,19 @@ 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 $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
+my $lifted_vcf = "$tmp_prefix.lifted.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 $unsorted_vcf -chain $chain -dict $newRef.dict";
+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 $cacheSize";
 system($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 $sorted_vcf -o $out";
+$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $lifted_vcf -o $out";
 system($cmd);
 
 # clean up
-unlink $unsorted_vcf;
-unlink $sorted_vcf;
+unlink $lifted_vcf;
 
 print "\nDone!\n";