diff --git a/perl/AnnotateVCFwithMAF.pl b/perl/AnnotateVCFwithMAF.pl
new file mode 100755
index 000000000..1e5dc2363
--- /dev/null
+++ b/perl/AnnotateVCFwithMAF.pl
@@ -0,0 +1,122 @@
+#!/usr/bin/perl -w
+
+use strict;
+use lib "$ENV{'STING_DIR'}/perl";
+use StingArgs;
+use Data::Dumper;
+
+my %args = &getCommandArguments("VCF_IN" => undef, "MAF_IN" => undef, "VCF_OUT" => "/dev/stdout");
+
+my %ignoreEntries = (
+    'normal_barcode' => 1,
+    'tumor_barcode' => 1,
+    'build' => 1,
+    'tum_allele1' => 1,
+    'ref_allele' => 1,
+    'tum_allele2' => 1,
+    'start' => 1,
+    'end' => 1,
+);
+
+my %maf;
+open(MAF_IN, $args{'MAF_IN'});
+
+chomp(my $mafheader = <MAF_IN>);
+chomp($mafheader);
+my @mafheader = split(/\s+/, $mafheader);
+
+while (my $mafline = <MAF_IN>) {
+    chomp($mafline);
+    my @mafline = split(/\s+/, $mafline);
+
+    my %mafentry;
+    for (my $i = 0; $i <= $#mafheader; $i++) {
+        $mafentry{$mafheader[$i]} = $mafline[$i];
+    }
+
+    my $locus = "$mafentry{'chr'}:$mafentry{'start'}";
+    if (exists($mafentry{$locus})) {
+        print "Locus $locus already spoken for!\n";
+        print Dumper(\%mafentry);
+        exit(1);
+    }
+
+    $maf{$locus} = \%mafentry;
+
+    #print Dumper(\%mafentry);
+}
+close(MAF_IN);
+
+open(VCF_OUT, ">$args{'VCF_OUT'}");
+open(VCF_IN, $args{'VCF_IN'});
+
+my @vcfheader;
+while (my $vcfline = <VCF_IN>) {
+    chomp($vcfline);
+
+    if ($vcfline =~ /##/) {
+        print VCF_OUT "$vcfline\n";
+    } elsif ($vcfline =~ /#CHROM/) {
+        print VCF_OUT "##source=AnnotateVCFwithMAF\n";
+        print VCF_OUT "##INFO=cDNAchange,1,String,cDNAchange\n";
+        print VCF_OUT "##INFO=classification,1,String,classification\n";
+        print VCF_OUT "##INFO=codonchange,1,String,codonchange\n";
+        print VCF_OUT "##INFO=gene,1,String,gene\n";
+        print VCF_OUT "##INFO=genomechange,1,String,genomechange\n";
+        print VCF_OUT "##INFO=proteinchange,1,String,proteinchange\n";
+        print VCF_OUT "##INFO=strand,1,String,strand\n";
+        print VCF_OUT "##INFO=transcript,1,String,transcript\n";
+        print VCF_OUT "##INFO=type,1,String,type\n";
+        print VCF_OUT "$vcfline\n";
+
+        $vcfline =~ s/#//g;
+        @vcfheader = split(/\s+/, $vcfline);
+    } else {
+        my @vcfentry = split(/\s+/, $vcfline);
+        my %vcfentry;
+
+        for (my $i = 0; $i <= $#vcfheader; $i++) {
+            $vcfentry{$vcfheader[$i]} = $vcfentry[$i];
+        }
+
+        my $locus = "$vcfentry{'CHROM'}:$vcfentry{'POS'}";
+        if (!exists($maf{$locus})) {
+            for (my $i = 1; $i <= 10; $i++) {
+                $locus = "$vcfentry{'CHROM'}:" . ($vcfentry{'POS'}-$i);
+
+                last if (exists($maf{$locus}));
+            }
+        }
+        my %mafentry = %{$maf{$locus}};
+
+        my @info = split(/;/, $vcfentry{'INFO'});
+        my %info;
+        foreach my $info (@info) {
+            my ($key, $value) = split(/=/, $info);
+
+            $info{$key} = $value;
+        }
+
+        foreach my $mafkey (sort { $a cmp $b } keys(%mafentry)) {
+            if (!$ignoreEntries{$mafkey}) {
+                $info{$mafkey} = $mafentry{$mafkey};
+            }
+        }
+
+        my @newinfo;
+        foreach my $infokey (sort { $a cmp $b } keys(%info)) {
+            push(@newinfo, "$infokey=$info{$infokey}");
+        }
+        $vcfentry{'INFO'} = join(";", @newinfo);
+
+        my @newvcfline;
+        for (my $i = 0; $i <= $#vcfheader; $i++) {
+            push(@newvcfline, $vcfentry{$vcfheader[$i]});
+        }
+
+        print VCF_OUT join("\t", @newvcfline) . "\n";
+    }
+}
+
+close(VCF_IN);
+close(VCF_OUT);