diff --git a/docs/SOP_alignment_variant_annotation.md b/docs/SOP_alignment_variant_annotation.md
index 37a6333944d6818960e0c30c0586de0e9ee56a4b..3e12d0154ffd0bcfb8515f92b78ef7a13855ebac 100644
--- a/docs/SOP_alignment_variant_annotation.md
+++ b/docs/SOP_alignment_variant_annotation.md
@@ -190,17 +190,18 @@ ped_file=<input_ped_file>
 ln -s $ped_file $project_id.ped
 ```
 
-3. In the params folder, create the symlinks to the reads and the bcbio configuration files. If specifying a common sample suffix, ensure it includes any joining characters, e.g. “-“ or “_”, so that the family identifier can be cleanly separated from the suffix. Get the number of families from the batch.
+3. In the params folder, create the symlinks to the reads and the bcbio configuration files. If specifying a common sample suffix, ensure it includes any joining characters, e.g. “-“ or “_”, so that the family identifier can be cleanly separated from the suffix. Get the number of families from the batch. Version should be "v1" by default for the first analysis run of a batch, "v2" etc for subsequent runs.
 
 
 ### Edinburgh Genomics data
 
 ```
 cd $PARAMS_DIR
+version=<version>
 sample_suffix=<sample_suffix>
 /home/u035/project/scripts/prepare_bcbio_config.sh \
   /home/u035/project/scripts/trio_whole_exome_config.sh \
-  $project_id $sample_suffix &> $project_id.log
+  $project_id $version $sample_suffix &> $project_id.log
 X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 ```
 
@@ -208,17 +209,19 @@ X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 
 ```
 cd $PARAMS_DIR
+version=<version>
+sample_suffix=<sample_suffix>
 /home/u035/project/scripts/prepare_bcbio_config_crf.sh \
   /home/u035/project/scripts/trio_whole_exome_crf_config.sh \
-  $project_id $sample_suffix &> $project_id.log
+  $project_id $version $sample_suffix &> $project_id.log
 X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 ```
 
-4. Submit the bcbio jobs from the logs folder.
+4. Submit the bcbio jobs from the logs folder. See above for version.
 
 ```
 cd /home/u035/project/trio_whole_exome/analysis/logs
-qsub -v PROJECT_ID=$project_id,\
+qsub -v PROJECT_ID=$project_id,VERSION=$version\
   CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
   -J 1-$X -N trio_whole_exome_bcbio.$project_id \
   /home/u035/project/scripts/submit_bcbio_trio_wes.sh
@@ -233,8 +236,8 @@ source /home/u035/project/scripts/trio_whole_exome_config.sh
 cd /scratch/u035/project/trio_whole_exome/analysis/output
 /home/u035/project/software/bcbio/anaconda/bin/multiqc --title "Trio whole exome QC report: $project_id" \
   --outdir qc \
-  --filename ${project_id}_qc_report.html \
-  *$project_id*
+  --filename ${version}_${project_id}_qc_report.html \
+  *$version*$project_id*
 ```
 
 6. Check the parent-child relationships predicted by peddy match the pedigree information. There should be no entries in the <EdGE_project_id>.ped_check.txt file that do not end in ‘True’. If there are, report these back to the NHS Clinical Scientist who generated the PED file for this batch. The batch id is the 5 digit number that prefixes all the family ids in the output.
@@ -245,8 +248,9 @@ perl /home/u035/project/scripts/trio_whole_exome_parse_peddy_ped_csv.pl \
   --output /scratch/u035/project/trio_whole_exome/analysis/output \
   --project $project_id \
   --batch $batch_id \
+  --version $version \
   --ped /scratch/u035/project/trio_whole_exome/analysis/params/$project_id.ped
-grep -v False$ qc/$project_id.ped_check.txt
+grep -v False$ qc/${version}_$project_id.ped_check.txt
 ```
 
 7. Clear the work directory and move the log files to the complete sub-directory.
@@ -268,5 +272,5 @@ cd /exports/igmm/datastore/IGMM-VariantAnalysis/documentation/trio_whole_exome/q
 user=<ultra_user_id>
 project_id=<EdGE_project_id>
 
-scp $user@ultra.epcc.ed.ac.uk:/scratch/u035/project/trio_whole_exome/analysis/output/qc/${project_id}_qc_report.html ./
+scp $user@ultra.epcc.ed.ac.uk:/scratch/u035/project/trio_whole_exome/analysis/output/qc/${version}_${project_id}_qc_report.html ./
 ```