From 240f711bab848e6426e96205620f2db692da1f81 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 16 Mar 2018 09:47:56 -0500
Subject: [PATCH] fix typos dnaseqalign cnvkit
---
alignment/dnaseqalign.sh | 2 +-
variants/cnvkit.sh | 10 ++++++----
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index ffa99c4..219f7f8 100644
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -12,7 +12,7 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :r:x:y:p:u:h opt
+while getopts :r:x:y:p:uh opt
do
case $opt in
r) index_path=$OPTARG;;
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index d4ba922..40b7218 100644
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -21,6 +21,8 @@ done
shift $(($OPTIND -1))
+index_path='/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/'
+
# Check for mandatory options
if [[ -z $pair_id ]] || [[ -z $sbam ]]; then
usage
@@ -33,13 +35,13 @@ baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh
module load cnvkit/0.9.0
-cnvkit.py coverage ${sbam} /project/shared/bicf_workflow_ref/GRCh38/UTSWV2.cnvkit_targets.bed -o ${pair_id}.targetcoverage.cnn
-cnvkit.py coverage ${sbam} /project/shared/bicf_workflow_ref/GRCh38/UTSWV2.cnvkit_antitargets.bed -o ${pair_id}.antitargetcoverage.cnn
+cnvkit.py coverage ${sbam} ${index_path}/UTSWV2.cnvkit_targets.bed -o ${pair_id}.targetcoverage.cnn
+cnvkit.py coverage ${sbam} ${index_path}/UTSWV2.cnvkit_antitargets.bed -o ${pair_id}.antitargetcoverage.cnn
if [[ $umi == 'umi' ]]
then
-cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn /project/shared/bicf_workflow_ref/GRCh38/UTSWV2.uminormals.cnn -o ${pair_id}.cnr
+cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${index_path}/UTSWV2.uminormals.cnn -o ${pair_id}.cnr
else
-cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn /project/shared/bicf_workflow_ref/GRCh38/UTSWV2.normals.cnn -o ${pair_id}.cnr
+cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${index_path}/UTSWV2.normals.cnn -o ${pair_id}.cnr
fi
cnvkit.py segment ${pair_id}.cnr -o ${pair_id}.cns
--
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