From 97de96e9a17eb7817cb04e890b240692b37c4d73 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sat, 8 Sep 2018 16:37:38 -0500
Subject: [PATCH] 4adapter readgroup bug
---
alignment/dnaseqalign.sh | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index 03579b0..d08cf71 100644
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -12,13 +12,14 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :r:x:y:p:uh opt
+while getopts :r:x:y:g:p:uh opt
do
case $opt in
r) index_path=$OPTARG;;
x) fq1=$OPTARG;;
y) fq2=$OPTARG;;
u) umi='umi';;
+ g) read_group=$OPTARG;;
p) pair_id=$OPTARG;;
h) usage;;
esac
@@ -36,6 +37,11 @@ then
SLURM_CPUS_ON_NODE=1
fi
+if [[ -z $read_group ]]
+then
+ read_group=$pair_id
+fi
+
source /etc/profile.d/modules.sh
module load bwakit/0.7.15 bwa/intel/0.7.15 samtools/1.6 picard/2.10.3
@@ -45,9 +51,9 @@ diff $fq1 $fq2 > difffile
if [ -s difffile ]
then
- bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} ${fq2} > out.sam
+ bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${read_group}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${read_group}" ${index_path}/genome.fa ${fq1} ${fq2} > out.sam
else
- bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} > out.sam
+ bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${read_group}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${read_group}" ${index_path}/genome.fa ${fq1} > out.sam
fi
if [[ $umi == 'umi' ]] && [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
--
GitLab