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Commit c49b6ffe authored by Brandi Cantarel's avatar Brandi Cantarel
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bug fixes

parent 98be9ebf
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variants/gatkrunner.sh
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View file @ c49b6ffe
...@@ -57,7 +57,7 @@ else ...@@ -57,7 +57,7 @@ else
fi fi
source /etc/profile.d/modules.sh 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} samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
if [[ $algo == 'gatkbam_rna' ]] if [[ $algo == 'gatkbam_rna' ]]
......
variants/uni_norm_annot.sh
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View file @ c49b6ffe
...@@ -15,6 +15,7 @@ do ...@@ -15,6 +15,7 @@ do
case $opt in case $opt in
r) index_path=$OPTARG;; r) index_path=$OPTARG;;
p) pair_id=$OPTARG;; p) pair_id=$OPTARG;;
v) vcf=$OPTARG;; v) vcf=$OPTARG;;
h) usage;; h) usage;;
esac esac
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