From ad7476ee64656983deb83301e439b6bd476513c5 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sun, 25 Nov 2018 07:54:14 -0600
Subject: [PATCH] updates to cnvkit
---
variants/cnvkit.sh | 2 +-
variants/filter_cnvkit.pl | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index 7129b70..98c3363 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -49,7 +49,7 @@ then
elif [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2_2.panelplus.bed' ]]
then
normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
- target='panel1385V2-2.cnvkit_'
+ targets="${index_path}/panel1385V2-2.cnvkit_"
fi
echo "${targets}targets.bed"
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index 6dfdf44..2f60eef 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -73,7 +73,7 @@ while (my $line = <CNR>) {
}
open IN, "<$file" or die $!;
-my $header = <IN>;
+$header = <IN>;
while (my $line = <IN>) {
chomp($line);
my ($chr,$start,$end,$geneids,$log2,$cn,$depth,
--
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