diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh index c1b936144c291fd8a7e54dfa6483289e95565f77..bd0e964fd4a65d2ebb9edb0231574495c579cc48 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 b2007aacec26549c0b890855b05d8f372dafde72..dba02f29f8ffdd1717d49e7f33f8b78caccb15be 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