From 9f6d0f8f5dbfb7501e70666215e4ffeafa633938 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 16 Apr 2019 09:26:11 -0500
Subject: [PATCH] adding rmdup bamqc
---
alignment/bamqc.sh | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index 029a921..91ddb95 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -8,11 +8,12 @@ usage() {
echo "-n --NucType"
echo "-p --Prefix for output file name"
echo "-c --Capture Bedfile"
+ echo "-d --RemoveDuplicates 1=yes, 0=no default=no"
echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/human/GRCh38 -b SRR1551047.bam -n dna -c target.bed"
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :r:b:c:n:p:h opt
+while getopts :r:b:c:n:p:d:h opt
do
case $opt in
r) index_path=$OPTARG;;
@@ -20,6 +21,7 @@ do
c) bed=$OPTARG;;
n) nuctype=$OPTARG;;
p) pair_id=$OPTARG;;
+ d) dedup=$OPTARG;;
h) usage;;
esac
done
@@ -42,6 +44,12 @@ then
SLURM_CPUS_ON_NODE=1
fi
+if [[ $dedup == 1 ]]
+then
+ mv $sbam ori.bam
+ samtools view -@ $SLURM_CPUS_ON_NODE -F 1024 -b -o ${sbam} ori.bam
+fi
+
if [[ $nuctype == 'dna' ]]; then
module load bedtools/2.26.0 picard/2.10.3
samtools view -@ $SLURM_CPUS_ON_NODE -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
--
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