diff --git a/docs/SOP_alignment_variant_annotation_ultra2.md b/docs/SOP_alignment_variant_annotation_ultra2.md
index 63157a060d77471b84802f4e090319c745c66e4e..4d09433ffde88cd638e48d58ed9c0133121e8fd8 100644
--- a/docs/SOP_alignment_variant_annotation_ultra2.md
+++ b/docs/SOP_alignment_variant_annotation_ultra2.md
@@ -161,8 +161,8 @@ X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 
 ```
 cd /home/u035/u035/shared/trio_whole_exome/analysis/logs
-qsub -v PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=/home/u035/u035/shared/scripts/trio_whole_exome_config.sh \
-  -J 1-$X -N trio_whole_exome_bcbio.$project_id \
+sbatch --export=PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=/home/u035/u035/shared/scripts/trio_whole_exome_config.sh \
+  --array=1-$X --job-name=trio_whole_exome_bcbio.$project_id \
   /home/u035/u035/shared/scripts/submit_bcbio_trio_wes.sh
 ```
 
diff --git a/submit_bcbio_trio_wes.sh b/submit_bcbio_trio_wes.sh
index d07d9eb2e101ec8727d043f892f93ba46582ea8b..9b096b38bb3b86880e4591733eb0c1d75b90c9d7 100755
--- a/submit_bcbio_trio_wes.sh
+++ b/submit_bcbio_trio_wes.sh
@@ -1,18 +1,19 @@
 #!/bin/bash
-#PBS -l walltime=48:00:00
-#PBS -l ncpus=16,mem=8gb
-#PBS -q sgp
-#PBS -N trio_whole_exome_bcbio
-#PBS -j oe
+#SBATCH --cpus-per-task 16
+#SBATCH --mem=8GB
+#SBATCH --time=48:00:00
+#SBATCH --job-name=trio_whole_exome_bcbio
+#SBATCH --output=trio_whole_exome_bcbio.%A_%a.out
+#SBATCH --error=trio_whole_exome_bcbio.%A_%a.err
 
 # enable running singletons
-if [ -z $PBS_ARRAY_INDEX ]
+if [ -z $SLURM_ARRAY_TASK_ID ]
 then
   if [ -z $INDEX ]
   then
-    export PBS_ARRAY_INDEX=1
+    export SLURM_ARRAY_TASK_ID=1
   else
-    export PBS_ARRAY_INDEX=$INDEX
+    export SLURM_ARRAY_TASK_ID=$INDEX
   fi
 fi
 
@@ -23,19 +24,23 @@ fi
 
 source $CONFIG_SH
 
-FAMILY_ID=`head -n $PBS_ARRAY_INDEX $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tail -n 1`
+FAMILY_ID=`head -n $SLURM_ARRAY_TASK_ID $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tail -n 1`
 
-CONFIG_FILE=$CONFIG_DIR/${VERSION}_${PROJECT_ID}_${FAMILY_ID}.yaml
+SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
+
+CONFIG_FILE=$CONFIG_DIR/${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}.yaml
 mkdir -p $WORK_DIR/$FAMILY_ID
 cd $WORK_DIR/$FAMILY_ID
 
-bcbio_nextgen.py $CONFIG_FILE -n 16 -t local
+bcbio_nextgen.py $CONFIG_FILE -n $SLURM_CPUS_PER_TASK -t local
+
+exit
 
 DATE=$(basename `tail log/bcbio-nextgen.log | grep 'Storing in local filesystem' | tail -n 1 | awk '{ print $6 }' | perl -pe "s/_${PROJECT_ID}.+//"`)
 
-if [ -e $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID} ]
+if [ -e $OUTPUT_DIR/${DATE}_${SHORT_PROJECT_ID}_${FAMILY_ID} ]
 then
-  for INDV in `cut -f 2 $PARAMS_DIR/${PROJECT_ID}_${FAMILY_ID}.ped`
+  for INDV in `cut -f 2 $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/params/${PROJECT_ID}_${FAMILY_ID}.ped`
   do
     mv $OUTPUT_DIR/$INDV $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}/
   done
@@ -53,4 +58,3 @@ then
 else
   echo $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID} does not exist.
 fi
-