--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFToolsStats/VCFToolsStats.pl	Mon Mar 23 05:53:20 2015 -0400
@@ -0,0 +1,71 @@
+
+#!/usr/bin/perl
+
+use strict;
+use Switch;
+use Getopt::Long;
+use Bio::SeqIO;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+
+where <args> are:
+
+    -i, --input          <VCF input>
+    -o, --out            <output basename>
+~;
+$usage .= "\n";
+
+my ($input,$out);
+
+GetOptions(
+	"input=s"        => \$input,
+	"out=s"          => \$out
+);
+
+
+die $usage
+  if ( !$input);
+
+
+
+my $nb_gene = `grep -c mRNA $input`;
+$nb_gene =~s/\n//g;
+my $nb_intergenic = `grep -c INTERGENIC $input`;
+$nb_intergenic =~s/\n//g;
+
+my $nb_intron = `grep -c INTRON $input`;
+$nb_intron =~s/\n//g;
+my $nb_UTR = `grep -c UTR $input`;
+$nb_UTR =~s/\n//g;
+my $nb_exon = $nb_gene - $nb_intron - $nb_UTR;
+
+my $nb_ns = `grep -c NON_SYNONYMOUS_CODING $input`;
+$nb_ns =~s/\n//g;
+my $nb_s = $nb_exon - $nb_ns;
+
+
+
+	
+#system("$VCFTOOLS_EXE --vcf $input --remove-filtered-all --out $out --hardy >>vcftools.log 2>&1");
+system("vcftools --vcf $input --remove-filtered-all --out $out --het >>vcftools.log 2>&1");
+system("vcftools --vcf $input --remove-filtered-all --out $out --TsTv-summary >>vcftools.log 2>&1");
+system("vcftools --vcf $input --remove-filtered-all --out $out --missing-indv >>vcftools.log 2>&1");
+
+open(my $G,">$out.annotation");
+print $G "Genic	$nb_gene\n";
+print $G "Intergenic	$nb_intergenic\n";
+print $G "========\n";
+print $G "Intron	$nb_intron\n";
+print $G "Exon	$nb_exon\n";
+print $G "UTR	$nb_UTR\n";
+print $G "========\n";
+print $G "Non-syn	$nb_ns\n";
+print $G "Synonym	$nb_s\n";
+close($G);
+
+
+
+
+
+	
+