From c49b6ffe4b376f1744ac48dbb8d3a317a3f773a9 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 20 May 2019 12:01:40 -0500
Subject: [PATCH] bug fixes
---
variants/gatkrunner.sh | 2 +-
variants/uni_norm_annot.sh | 1 +
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index c1b9361..bd0e964 100755
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -57,7 +57,7 @@ else
fi
source /etc/profile.d/modules.sh
-module load gatk/4.2.1.0 samtools/gcc/1.8
+module load gatk/4.1.2.0 samtools/gcc/1.8
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
if [[ $algo == 'gatkbam_rna' ]]
diff --git a/variants/uni_norm_annot.sh b/variants/uni_norm_annot.sh
index b2007aa..dba02f2 100644
--- a/variants/uni_norm_annot.sh
+++ b/variants/uni_norm_annot.sh
@@ -15,6 +15,7 @@ do
case $opt in
r) index_path=$OPTARG;;
p) pair_id=$OPTARG;;
+
v) vcf=$OPTARG;;
h) usage;;
esac
--
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