zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Write headers that are VCF4.0 compliant 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4213 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-09-03 23:46:27 +00:00
parent ef7454a241
commit e9af893bf4
1 changed files with 16 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

26
perl/AnnotateVCFwithMAF.pl
View File

@ -1,6 +1,7 @@
#!/usr/bin/perl -w
use strict;
use Data::Dumper;
sub usage {
print "Usage: $0 <input.vcf> <input.maf> <output.vcf>\n";
@ -62,16 +63,17 @@ while (my $vcfline = <VCF_IN>) {
if ($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 "##INFO=<ID=cDNAchange,Number=1,Type=String,Description=\"cDNAchange\">\n";
print VCF_OUT "##INFO=<ID=classification,Number=1,Type=String,Description=\"classification\">\n";
print VCF_OUT "##INFO=<ID=codonchange,Number=1,Type=String,Description=\"codonchange\">\n";
print VCF_OUT "##INFO=<ID=gene,Number=1,Type=String,Description=\"gene\">\n";
print VCF_OUT "##INFO=<ID=genomechange,Number=1,Type=String,Description=\"genomechange\">\n";
print VCF_OUT "##INFO=<ID=proteinchange,Number=1,Type=String,Description=\"proteinchange\">\n";
print VCF_OUT "##INFO=<ID=strand,Number=1,Type=String,Description=\"strand\">\n";
print VCF_OUT "##INFO=<ID=transcript,Number=1,Type=String,Description=\"transcript\">\n";
print VCF_OUT "##INFO=<ID=type,Number=1,Type=String,Description=\"type\">\n";
print VCF_OUT "$vcfline\n";
$vcfline =~ s/#//g;
@ -110,7 +112,11 @@ while (my $vcfline = <VCF_IN>) {
my @newinfo;
foreach my $infokey (sort { $a cmp $b } keys(%info)) {
push(@newinfo, "$infokey=$info{$infokey}");
if (!defined($info{$infokey})) {
#print "$infokey is missing\n";
} else {
push(@newinfo, "$infokey=$info{$infokey}");
}
}
$vcfentry{'INFO'} = join(";", @newinfo);