From 4222e4aa236c5a43feb1af23649ef92b374f47a3 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 27 Feb 2019 20:41:16 -0600
Subject: [PATCH] update reference location
---
alignment/dnaseqalign.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index aecb7e3..36a1364 100644
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -56,7 +56,7 @@ else
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' ]]
+if [[ $umi == 'umi' ]] && [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38' ]]
then
k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p tmphla ${index_path}/genome.fa.alt out.sam | python ${baseDir}/add_umi_sam.py -s - -o output.unsort.bam
elif [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38' ]]
--
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