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One more fix: exclude input VCF file's directory name from the output file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4226 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-09-08 03:09:08 +00:00
parent 594fb4a547
commit 84ddadca64
1 changed files with 2 additions and 1 deletions
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3
perl/AnnotateVCFwithMAF.pl
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@ -2,6 +2,7 @@
use strict; use strict;
use Data::Dumper; use Data::Dumper;
use File::Basename;
sub usage { sub usage {
print "Usage: $0 <input.vcf> <input.maf> <output.vcf>\n"; print "Usage: $0 <input.vcf> <input.maf> <output.vcf>\n";
@ -16,7 +17,7 @@ if (!defined($args{'VCF_IN'}) || !defined($args{'MAF_IN'})) {
&usage(); &usage();
} }
($args{'VCF_OUT'} = $args{'VCF_IN'}) =~ s/\.vcf/.maf_annotated.vcf/; ($args{'VCF_OUT'} = basename($args{'VCF_IN'})) =~ s/\.vcf/.maf_annotated.vcf/;
my %ignoreEntries = ( my %ignoreEntries = (
'normal_barcode' => 1, 'normal_barcode' => 1,