From b6d2f6898ecc1890b4df305e9505bdaa5eace4a6 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 12 Mar 2018 11:57:59 -0500
Subject: [PATCH] update db location
---
variants/filter_cnvkit.pl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index cbd46a3..596ec22 100644
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -2,13 +2,13 @@
#parse_cnvkit_table.pl
my $refdir = '/project/shared/bicf_workflow_ref/GRCh38/';
-open OM, "<$refdir\/panel1385.genelist.txt" or die $!;
+open OM, "<$refdir\/clinseq_prj/panel1385.genelist.txt" or die $!;
while (my $line = <OM>) {
chomp($line);
$keep{$line} = 1;
}
-open ENT_ENS, "</project/shared/bicf_workflow_ref/gene2ensembl.human.txt" or die $!;
+open ENT_ENS, "<$refdir/../gene2ensembl.human.txt" or die $!;
my %entrez;
my $ent_header = <ENT_ENS>;
while (my $line = <ENT_ENS>){
@@ -17,7 +17,7 @@ while (my $line = <ENT_ENS>){
$entrez{$row[2]}=$row[1];
}
close ENT_ENS;
-open ENT_SYM, "</project/shared/bicf_workflow_ref/gene_info.human.txt" or die $!;
+open ENT_SYM, "<$refdir/../gene_info.human.txt" or die $!;
$ent_header = <ENT_SYM>;
while (my $line = <ENT_SYM>){
chomp $line;
--
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