From e068e8325760f19e593153ce8e7d7a4b15a50369 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 13 Aug 2019 17:59:28 -0500
Subject: [PATCH] moving out normal/target initialization
---
variants/cnvkit.sh | 20 +++-----------------
1 file changed, 3 insertions(+), 17 deletions(-)
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index 7ae4b16..f52e505 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -43,26 +43,12 @@ then
fi
if [[ -z $normals ]] || [[ -z $targets ]]
then
- if [[ $capture == "${index_path}/UTSWV2.bed" ]]
- then
- normals="${index_path}/UTSWV2.normals.cnn"
- targets="${index_path}/UTSWV2.cnvkit_"
- if [[ $umi == 'umi' ]]
- then
- normals="${index_path}/UTSWV2.uminormals.cnn"
- fi
- elif [[ $capture == "${index_path}/UTSWV2_2.panelplus.bed" ]]
- then
- normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
- targets="${index_path}/panel1385V2-2.cnvkit_"
- elif [[ $capture == "${index_path}/hemepanelV3.bed" ]]
- then
- normals="${index_path}/hemepanelV3.panelofnormals.cnn"
- targets="${index_path}/hemepanelV3.cnvkit_"
- fi
+ usage
fi
+
echo "${targets}targets.bed"
echo "${targets}antitargets.bed"
+echo "${normals}"
source /etc/profile.d/modules.sh
module load cnvkit/0.9.5 bedtools/2.26.0
--
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