From ec7b3630470f5beddda8bf6ca9bda73962a6419c Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <b.cantarel@gmail.com>
Date: Fri, 18 Sep 2020 10:47:38 -0500
Subject: [PATCH] adding abra2
---
alignment/abra2.sh | 58 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
create mode 100755 alignment/abra2.sh
diff --git a/alignment/abra2.sh b/alignment/abra2.sh
new file mode 100755
index 0000000..228910d
--- /dev/null
+++ b/alignment/abra2.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+#gatkrunner.sh
+
+usage() {
+ echo "-h Help documentation for gatkrunner.sh"
+ echo "-r --Reference Genome: GRCh38 or GRCm38"
+ echo "-b --BAM File"
+ echo "-p --Prefix for output file name"
+ echo "-a --Algorithm/Command"
+ echo "Example: bash hisat.sh -p prefix -r GRCh38 -b File.bam"
+ exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :r:a:c:b:p:h opt
+do
+ case $opt in
+ r) index_path=$OPTARG;;
+ b) sbam=$OPTARG;;
+ p) pair_id=$OPTARG;;
+ c) tbed==$OPTARG;;
+ h) usage;;
+ esac
+done
+
+shift $(($OPTIND -1))
+
+# Check for mandatory options
+if [[ -z $pair_id ]] || [[ -z $sbam ]] || [[ -z $index_path ]]
+then
+ usage
+fi
+
+NPROC=$SLURM_CPUS_ON_NODE
+if [[ -z $NPROC ]]
+then
+ NPROC=`nproc`
+fi
+
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load abra2/2.18 samtools/gcc/1.8
+ abrajar=/cm/shared/apps/abra2/lib/abra2.jar
+else
+ abrajar=/usr/local/bin/abra2.jar
+fi
+ioopt="--in ${sbam} --out ${pair_id}.abra2.bam"
+opt=''
+if [ -n "$tbed" ]
+then
+ opt="--targets $tbed"
+fi
+
+which samtools
+samtools index -@ $NPROC ${sbam}
+mkdir tmpdir
+java -Xmx16G -jar ${abrajar} ${ioopt} --ref ${index_path}/genome.fa --threads $NRPOC $opt --tmpdir tmpdir --mbq 150 --mnf 5 --mer 0.05 > abra.log
+samtools index -@ $NPROC ${pair_id}.abra2.bam
--
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