diff --git a/docs/SOP_alignment_variant_annotation_ultra2.md b/docs/SOP_alignment_variant_annotation_ultra2.md
index fbfa22416be2c997d32a435813fbcc80c7ca24b4..be3d2d17a0af438003fd91fa2c58e6df285f886d 100644
--- a/docs/SOP_alignment_variant_annotation_ultra2.md
+++ b/docs/SOP_alignment_variant_annotation_ultra2.md
@@ -1,34 +1,24 @@
 # Standard operating procedure - Alignment, variant calling, and annotation of trio whole exome samples at the Edinburgh Parallel Computing Centre
 
-This SOP applies to batches of family/trio samples where trio whole exome sequencing has been performed by Edinburgh Genomics (EdGE) or the Edinburgh Clinical Research Facility (ECRF). It assumes that data has been successfully transferred to the Edinburgh Parallel Computing Centre (EPCC) (see SOP: Transfer of whole exome sequencing samples from Edinburgh Genomics to Edinburgh Parallel Computing Centre). Scripts are version controlled on the University of Edinburgh gitlab server gitlab.ecdf.ed.ac.uk/igmmbioinformatics/trio-whole-exome. Request access by e-mail: alison.meynert@igmm.ed.ac.uk.
+This SOP applies to batches of family/trio samples where trio whole exome sequencing has been performed by Edinburgh Genomics (EdGE) or the Edinburgh Clinical Research Facility (ECRF). It assumes that data has been successfully transferred to the Edinburgh Parallel Computing Centre (EPCC) (see SOP: Transfer of whole exome sequencing samples from Edinburgh Genomics to Edinburgh Parallel Computing Centre). Scripts are version controlled on the University of Edinburgh gitlab server `gitlab.ecdf.ed.ac.uk/igmmbioinformatics/trio-whole-exome`. Request access by e-mail: alison.meynert@igmm.ed.ac.uk.
 
 ## Definitions
 
 In this document, N is the total number of samples in the project, and X is the number of families.
 
-Text in angle brackets, e.g. <project> indicates variable parameters. A variable parameter such as <family1-X> indicates that there are X instances of the parameter, each with their own unique value.
+Text in angle brackets, e.g. `<project>` indicates variable parameters. A variable parameter such as `<family1-X>` indicates that there are X instances of the parameter, each with their own unique value.
 
 ## Software and data requirements
 
-The analysis is run with the bcbio pipeline (version 1.2.3) located at /home/u035/project/software/bcbio. All genome reference and annotation data resources are contained within the genomes/Hsapiens/hg38 subfolder.
+The analysis is run with the bcbio pipeline (version 1.2.8) located at `/home/u035/u035/shared/software/bcbio`. All genome reference and annotation data resources are contained within the `genomes/Hsapiens/hg38` subfolder.
 
-The TWIST target BED file is at: /home/u035/project/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
-
-To generate the target BED file, first copy the file Twist_Exome_RefSeq_targets_hg38.bed from NHS Clinical Genetics Services to /home/u035/project/resources on ultra, then pad it by 15bp each side.
-
-```
-cd /home/u035/project/resources
-source ../scripts/trio_whole_exome_config.sh
-
-bedtools slop -g $REFERENCE_GENOME.fai -i Twist_Exome_RefSeq_targets_hg38.bed -b 15 | \
-  bedtools merge > Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
-```
+The TWIST target BED file is at: `/home/u035/u035/shared/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed`. See [resources](https://git.ecdf.ed.ac.uk/igmmbioinformatics/trio-whole-exome/blob/master/docs/Resources_ultra2.md).
 
 ## Input
 
 ### PED file
 
-A 6-column tab-delimited PED/FAM format file (https://www.cog-genomics.org/plink2/formats#fam) is required for each batch, describing the relationships between the sampled individuals, their sex, and their affected/unaffected status.
+A 6-column tab-delimited [PED/FAM format file](https://www.cog-genomics.org/plink2/formats#fam) is required for each batch, describing the relationships between the sampled individuals, their sex, and their affected/unaffected status.
 
 
 ### Sample id format
@@ -39,35 +29,32 @@ The sequencing reads for the samples delivered from EdGE are identified by folde
 <pcr_plate_id>_<indiv_id>_<family_id><suffix>
 ```
 
-The suffix identifies the exome kit, e.g. "_IDT-A". These identifiers are referenced below in the output file structure.
+The suffix identifies the exome kit, e.g. `_WESTwist_IDT-A`. These identifiers are referenced below in the output file structure.
 
 ### Reads - Edinburgh Genomics
 
-A set of paired end FASTQ files (designated by R1 or R2 suffixes), possibly more than one pair per sample. Each sample's files are in its own folder. The input files will be in the folder /scratch/u035/project/trio_whole_exome/data and follow the structure in *Figure 1*.
+A set of paired end FASTQ files (designated by R1 or R2 suffixes), possibly more than one pair per sample. Each sample's files are in its own folder. The input files will be in the folder `/home/u035/u035/shared/data` and follow the structure in *Figure 1*. Older deliveries contained the `<dated_batch>` folder within a `raw_data` folder.
 
 ```
 <EdGE_project_id>/
+  +---<dated_batch>/
+  |   +---<sample_id>/
+  |   |   +---*.fastq.count
+  |   |   +---*.fastq.gz
+  |   +---file_list.tsv
+  |   +---md5sums.txt
+  +---<dated_batch>_tree.txt
+  +---Information.txt
   +---md5_check.txt
-  +---raw_data/
-  |   +---<dated_batch>/
-  |   |   +---<EdGE_sample_id>/
-  |   |   |   +---<fastq_id>_R1.fastq.count
-  |   |   |   +---<fastq_id>_R1.fastq.gz
-  |   |   |   +---<fastq_id>_R2.fastq.count
-  |   |   |   +---<fastq_id>_R2.fastq.gz
-  |   |   +---file_list.tsv
-  |   |   +---md5sums.txt
-  |   +---<dated_batch>_tree.txt
-  |   +---Information.txt
-```
-*Figure 1.* File name and directory structure for a batch of sequencing from Edinburgh Genomics. The EdGE project id takes the format XXXXX_Lastname_Firstname, identifying the NHS staff member who submitted the samples for sequencing. The dated batch is in the format yyyymmdd – in general we expect there to be only one of these per EdGE project id. The FASTQ file id relates to the sequencing run information and does not contain any information about the sample itself.
+```
+*Figure 1.* File name and directory structure for a batch of sequencing from Edinburgh Genomics. The EdGE project id takes the format `XXXXX\_Lastname\_Firstname`, identifying the NHS staff member who submitted the samples for sequencing. The dated batch is in the format `yyyymmdd` – in general we expect there to be only one of these per EdGE project id. The FASTQ file names relate to the sequencing run information and do not contain any information about the sample itself.
 
 ### Reads - Edinburgh Clinical Research Facility
 
-A set of paired end FASTQ files (designated by R1 or R2 suffixes), generally one pair per sample. The input files will be in the folder /scratch/u035/project/trio_whole_exome/data and follow the structure in *Figure 2*.
+A set of paired end FASTQ files (designated by R1 or R2 suffixes), generally one pair per sample. The input files will be in the folder `/home/u035/u035/shared/data` and follow the structure in *Figure 2*.
 
 ```
-<EdGE_project_id>/
+<ECRF_project_id>/
   +---<internal_id_-md5.txt
   +---<pcr_plate_id>_<indiv_id>_<family_id><suffix>_S<i>_L001_R1_001.fastq.gz
   +---<pcr_plate_id>_<indiv_id>_<family_id><suffix>_S<i>_L001_R2_001.fastq.gz
@@ -78,21 +65,20 @@ A set of paired end FASTQ files (designated by R1 or R2 suffixes), generally one
 
 ## Working directories
 
-The project working directories will be in the folder /scratch/u035/project/trio_whole_exome/analysis and follow the structure in *Figure 3*.
+The project working directories will be in the folder `/home/u035/u035/shared/analysis` and follow the structure in *Figure 3*.
 
 ```
     config – bcbio configuration files in YAML format
     logs – PBS job submission log files
-    output – output to be passed to variant prioritization and archiving
     params – parameters for PBS job submission
-    reads – symlinks to input FASTQ files
+    reads – symlinks/merged versions of input FASTQ files
     work – bcbio working folder
 ```
 *Figure 3.* Project working directories.
 
 ## Project configuration
 
-A configuration script sets environment variables common to scripts used in this SOP. This is stored at /home/u035/project/scripts/trio_whole_exome_config.sh.
+A configuration script sets environment variables common to scripts used in this SOP. This is stored at `/home/u035/u035/shared/scripts/trio_whole_exome_config.sh`.
 
 ```
 #!/usr/bin/bash
@@ -100,27 +86,25 @@ A configuration script sets environment variables common to scripts used in this
 # Basic configuration options for trio WES pipeline
 #
 
-SCRIPTS=/home/u035/project/scripts
+BASE=/home/u035/u035/shared
+SCRIPTS=$BASE/scripts
 BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_template.yaml
-TARGET=/home/u035/project/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
-DOWNLOAD_DIR=/scratch/u035/project/trio_whole_exome/data
-REFERENCE_GENOME=/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
-
-BASE=/scratch/u035/project/trio_whole_exome/analysis
-PARAMS_DIR=$BASE/params
-READS_DIR=$BASE/reads
-CONFIG_DIR=$BASE/config
-WORK_DIR=$BASE/work
-OUTPUT_DIR=$BASE/output
+TARGET=$BASE/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+DOWNLOAD_DIR=$BASE/data
+REFERENCE_GENOME=$BASE/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
-ARCHIVE_DIR=/archive/u035/trio_whole_exome
+PARAMS_DIR=$BASE/analysis/params
+READS_DIR=$BASE/analysis/reads
+CONFIG_DIR=$BASE/analysis/config
+WORK_DIR=$BASE/analysis/work
+OUTPUT_DIR=$BASE/analysis/results
 
-export PATH=/home/u035/project/software/bcbio/tools/bin:$PATH
+export PATH=$BASE/software/bcbio/tools/bin:$PATH
 ````
 
 ## Template for bcbio configuration
 
-Bcbio requires a template file in YAML format to define the procedures run in the pipeline. The template for this project is stored at /home/u035/project/scripts/trio_whole_exome_bcbio_template.yaml.
+Bcbio requires a template file in YAML format to define the procedures run in the pipeline. The template for this project is stored at `/home/u035/u035/shared/scripts/trio_whole_exome_bcbio_template.yaml`.
 
 ```
 details:
@@ -141,7 +125,7 @@ details:
   analysis: variant2
   genome_build: hg38
 upload:
-  dir: /scratch/u035/project/trio_whole_exome/analysis/output
+  dir: /home/u035/u035/shared/results
 ```
 
 ## Output
@@ -149,10 +133,10 @@ upload:
 Per sample: BAM file of aligned reads against the hg38 genome assembly
 Per family: Annotated VCF file and QC report
 
-Output will be in the folder /scratch/u035/project/trio_whole_exome/analysis/output and follow the structure in *Figure 4* (with multiple instances of the indiv_id sub directories, one per sequenced family member.). The qc sub-directories are not enumerated, and automatically generated index files are not listed for brevity. An additional directory at the root of the output folder called “qc” will contain the MultiQC reports generated for an entire batch.
+Output will be in the folder `/home/u035/u035/shared/results/<version>_<project_id>` and follow the structure in *Figure 4* (with multiple instances of the indiv_id sub directories, one per sequenced family member.). The qc sub-directories are not enumerated, and automatically generated index files are not listed for brevity. An additional directory at the root of the output folder called “qc” will contain the MultiQC reports generated for an entire batch.
 
 ```
-<analysis_date>_<EdGE_project_id>_<pcr_plate_id>_<family_id>/
+<analysis_date>_<project_id>_<pcr_plate_id>_<family_id>/
   +---<indiv_id>_<family_id>/
   |   +---<indiv_id>_<family_id>-callable.bed
   |   +---<indiv_id>_<family_id>-ready.bam
@@ -178,11 +162,11 @@ Output will be in the folder /scratch/u035/project/trio_whole_exome/analysis/out
 1. Set environment variable project_id and general configuration variables.
 
 ```
-project_id=<EdGE_project_id>
-source /home/u035/project/scripts/trio_whole_exome_config.sh
+project_id=<project_id>
+source /home/u035/u035/shared/scripts/trio_whole_exome_config.sh
 ```
 
-2. Copy the PED file for the batch to the params folder in the working area. It should be named <EdGE_project_id>.ped, relating it to the input directory for the FASTQ files. If the PED file given was not named in this way, don’t rename it, create a symlink with the correct name.
+2. Copy the PED file for the batch to the params folder in the working area. It should be named <project_id>.ped, relating it to the input directory for the FASTQ files. If the PED file given was not named in this way, don’t rename it, create a symlink with the correct name.
 
 ```
 cd $PARAMS_DIR
@@ -199,8 +183,8 @@ ln -s $ped_file $project_id.ped
 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 \
+/home/u035/u035/shared/scripts/prepare_bcbio_config.sh \
+  /home/u035/u035/shared/scripts/trio_whole_exome_config.sh \
   $project_id $version $sample_suffix &> ${version}_${project_id}.log
 X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 ```
@@ -211,8 +195,8 @@ 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 \
+/home/u035/u035/shared/scripts/prepare_bcbio_config_crf.sh \
+  /home/u035/u035/shared/scripts/trio_whole_exome_crf_config.sh \
   $project_id $version $sample_suffix &> ${version}_${project_id}.log
 X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 ```
@@ -220,53 +204,65 @@ X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 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=$project_id,VERSION=$version,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
+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 \
-  /home/u035/project/scripts/submit_bcbio_trio_wes.sh
+  /home/u035/u035/shared/scripts/submit_bcbio_trio_wes.sh
 ```
 
 If all log files end in ‘Finished’ or ‘Storing in local filesystem’ for a metadata file (occasionally the job completes without quite outputting all of the ‘Storing’ messages), the batch is complete. If this is not the case, resubmit the incomplete jobs – they will resume where they left off.
 
-5. Generate a MultiQC report for all files in the batch.
+5. Clean up the output directory.
 
 ```
-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 \
+cd /home/u035/u035/shared/results
+short_project_id=`echo $project_id | cut -f 1 -d '_'`
+mkdir ${version}_${short_project_id}
+mv *${version}_${project_id}* ${version}_${short_project_id}/
+```
+
+6. Generate a MultiQC report for all files in the batch.
+
+```
+source /home/u035/u035/shared/scripts/trio_whole_exome_config.sh
+short_project_id=`echo $project_id | cut -f 1 -d '_'`
+
+cd /home/u035/u035/shared/results
+/home/u035/u035/shared/software/bcbio/anaconda/bin/multiqc --title "Trio whole exome QC report: $project_id" \
+  --outdir ${short_version}_${project_id}/qc \
   --filename ${version}_${project_id}_qc_report.html \
-  *$version*$project_id*
+  ${version}_${short_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.
+7. 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.
 
 ```
-cd /scratch/u035/project/trio_whole_exome/analysis/output
-perl /home/u035/project/scripts/trio_whole_exome_parse_peddy_ped_csv.pl \
-  --output /scratch/u035/project/trio_whole_exome/analysis/output \
+cd /home/u035/u035/shared/results
+short_project_id=`echo $project_id | cut -f 1 -d '_'`
+
+perl /home/u035/u035/shared/scripts/trio_whole_exome_parse_peddy_ped_csv.pl \
+  --output /home/u035/u035/shared/results/${version}_${short_project_id}/qc \
   --project $project_id \
   --batch $batch_id \
   --version $version \
-  --ped /scratch/u035/project/trio_whole_exome/analysis/params/$project_id.ped
-grep -v False$ qc/${version}_$project_id.ped_check.txt
+  --ped /home/u035/u035/shared/analysis/params/$project_id.ped
+grep -v False$ ${version}_${short_project_id}/qc/${version}_${project_id}.ped_check.txt
 ```
 
-7. Clean up the output directory.
+8. Clear the work directory and move the log files to the complete sub-directory.
 
 ```
-cd /home/u035/project/trio_whole_exome/
-mkdir ${version}_${project_id}
-mv *${version}_${project_id}* ${version}_${project_id}/
+cd /home/u035/u035/shared/analysis/work
+rm -r *
+cd /home/u035/u035/shared/analysis/logs
+mv trio_whole_exome_bcbio.$project_id* complete/
 ```
 
-8. Clear the work directory and move the log files to the complete sub-directory.
+9. Clean up the reads directory. Retain reads for samples in families where one sample has failed QC, using a list `retain\_for\_rerun.txt`. These will likely be required for later runs, and it is simpler to regenerate config YAML files if it is not necessary to re-do symlinks/read merging.
 
 ```
-cd /scratch/u035/project/trio_whole_exome/work
-rm -r *
-cd /home/u035/project/trio_whole_exome/logs
-mv trio_whole_exome_bcbio.$project_id* complete/
+cd /home/u035/u035/shared/analysis/reads/${project_id}
+rm `ls | grep -v -f retain_for_rerun.txt`
 ```
 
 9. Copy the MultiQC report to the IGMM-VariantAnalysis area on the IGMM datastore.
@@ -279,5 +275,5 @@ cd /exports/igmm/datastore/IGMM-VariantAnalysis/documentation/trio_whole_exome/q
 user=<ultra_user_id>
 project_id=<EdGE_project_id>
 
-scp $user@ultra.epcc.ed.ac.uk:/scratch/u035/project/trio_whole_exome/analysis/output/qc/${version}_${project_id}_qc_report.html ./
+scp $user@sdf-cs1.epcc.ed.ac.uk:/home/u035/u035/shared/results/${version}_${project_id}/qc/${version}_${project_id}_qc_report.html ./
 ```