From 2fa359f8bb6e6d2ea96740e56f96ea47f9a35308 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 7 Apr 2020 13:33:53 -0500
Subject: [PATCH] add msisensor2
---
variants/msisensor.sh | 42 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
create mode 100755 variants/msisensor.sh
diff --git a/variants/msisensor.sh b/variants/msisensor.sh
new file mode 100755
index 0000000..0b2f13f
--- /dev/null
+++ b/variants/msisensor.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+#svcalling.sh
+
+usage() {
+ echo "-h Help documentation for gatkrunner.sh"
+ echo "-r --Path to Reference Genome with the file genome.fa"
+ echo "-p --Prefix for output file name"
+ echo "Example: bash svcalling.sh -p prefix -r /path/GRCh38 -a gatk"
+ exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :r:l:p:h opt
+do
+ case $opt in
+ r) index_path=$OPTARG;;
+ p) pair_id=$OPTARG;;
+ b) sbam=$OPTARG;;
+ n) normal=$OPTARG;;
+ h) usage;;
+ esac
+done
+function join_by { local IFS="$1"; shift; echo "$*"; }
+
+shift $(($OPTIND -1))
+baseDir="`dirname \"$0\"`"
+
+
+# Check for mandatory options
+if [[ -z $tumor ]] || [[ -z $index_path ]]; then
+ usage
+
+source /etc/profile.d/modules.sh
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
+
+if [[ -n $normal ]]
+then
+ msisensor2 msi -d ${index_path}/microsatellites.list -n $normal -t $sbam -o ${pair_id}.msi
+
+else
+ # -M ${index_path}/msi_tumoronly_model
+ msisensor2 msi -d ${index_path}/microsatellites.list -t $sbam -o ${pair_id}.msi
+fi
--
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