Mercurial > repos > fcaramia > jointsnvmix

comparison jsm_to_vcf.pl @ 0:a1034918ab9b draft

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author fcaramia
date Thu, 20 Jun 2013 00:03:08 -0400
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-1:000000000000 0:a1034918ab9b
1 die qq(
2 Bad numbr of inputs
3
4 ) if(!@ARGV);
5
6 my $input=$ARGV[0];
7 my $vcf=$ARGV[1];
8
9
10 # Convert output to VCF format
11 open(FH, $input) or die "Couldn't open jsm file $input!\n";
12 open(OUT, ">$vcf") or die "Couldn't create vcf file $vcf!\n";
13
14 # print the vcf format we are using
15 print OUT "##fileformat=VCFv4.1\n";
16
17 # grab header which is the first line after the comment lines which start with ##
18 my $header = <FH>;
19 while(grep(/^##/, $header))
20 {
21 $header = <FH>;
22 }
23 my @head = split("\t", $header);
24
25 print "Converting jsm output to vcf\n";
26 # vcf header is
27 # #CHROM POS ID REF ALT QUAL FILTER INFO
28 print OUT "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
29 # for each line in jsm transform to vcf, any columns not in vcf concatenate them
30 # together and place them in the info column
31 while (my $line = <FH>)
32 {
33 chomp $line;
34 my @fields = split("\t", $line);
35 # create info column
36 # tumor_name=MH208_TUMOR;normal_name=MH208_LIVER;...;n_alt_sum=702
37 my @info;
38 for(my $index = 4; $index < $#fields; $index++)
39 {
40 push @info, "$head[$index]=$fields[$index]";
41 }
42 my $infofield = join(";", @info);
43 $fields[-1] = "PASS";
44
45 # print the line
46 print OUT "$fields[0]\t$fields[1]\t.\t$fields[2]\t$fields[3]\t.\t$fields[-1]\t$infofield\n";
47 }
48 close(FH);
49 close(OUT);