--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jsm_to_vcf.pl	Thu Jun 20 00:03:08 2013 -0400
@@ -0,0 +1,49 @@
+die qq(
+Bad numbr of inputs
+
+) if(!@ARGV);
+
+my $input=$ARGV[0];
+my $vcf=$ARGV[1];
+
+
+# Convert output to VCF format
+open(FH, $input) or die "Couldn't open jsm file $input!\n";
+open(OUT, ">$vcf") or die "Couldn't create vcf file $vcf!\n";
+
+# print the vcf format we are using
+print OUT "##fileformat=VCFv4.1\n";
+
+# grab header which is the first line after the comment lines which start with ##
+my $header = <FH>;
+while(grep(/^##/, $header)) 
+{
+	$header = <FH>;
+}
+my @head = split("\t", $header);
+
+print "Converting jsm output to vcf\n";
+# vcf header is
+# #CHROM POS ID REF ALT QUAL FILTER INFO
+print OUT "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
+# for each line in jsm transform to vcf, any columns not in vcf concatenate them
+# together and place them in the info column
+while (my $line = <FH>) 
+{
+	chomp $line;
+	my @fields = split("\t", $line);
+	# create info column
+	# tumor_name=MH208_TUMOR;normal_name=MH208_LIVER;...;n_alt_sum=702
+	my @info;
+	for(my $index = 4; $index < $#fields; $index++) 
+	{
+		push @info, "$head[$index]=$fields[$index]";
+	} 
+	my $infofield = join(";", @info);
+	$fields[-1] = "PASS";
+	
+	# print the line
+	print OUT "$fields[0]\t$fields[1]\t.\t$fields[2]\t$fields[3]\t.\t$fields[-1]\t$infofield\n";
+}
+close(FH);
+close(OUT);