add msisensor2

variants/msisensor.sh

+#!/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