bug fixes

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' ]]

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