diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl
index 5a34594d1..6e3b0fccf 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -54,11 +54,11 @@ while ( $inHeader == 1 ) {
     }
 }
 close(UNSORTED);
-
-$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai";
-print SORTED `$cmd`;
 close(SORTED);
 
+$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai >> $sorted_vcf";
+system($cmd);
+
 # 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";