diff --git a/NHS_WES_check_PED_aff_probands.py b/NHS_WES_check_PED_aff_probands.py
index 2ca0e8a33ed3507d234465c02a4b859761c97d5e..a3c84d3351dd038ab29500c240a64d856e09856b 100755
--- a/NHS_WES_check_PED_aff_probands.py
+++ b/NHS_WES_check_PED_aff_probands.py
@@ -59,6 +59,6 @@ if __name__ == '__main__':
     if len(sys.argv) == 2:
         go(sys.argv[1])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_check_PED_aff_probands.py a_ped_file"
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_check_PED_aff_probands.py a_ped_file"
         raise SystemExit
 
diff --git a/NHS_WES_check_PED_quad.py b/NHS_WES_check_PED_quad.py
index 1603c4678d7c63b09144ac83b4007a5dd351f16f..998f4d01cf778abb2e6caf3e99f5bb89f529e40c 100755
--- a/NHS_WES_check_PED_quad.py
+++ b/NHS_WES_check_PED_quad.py
@@ -69,6 +69,6 @@ if __name__ == '__main__':
     if len(sys.argv) == 2:
         go(sys.argv[1])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_check_PED_quad.py a_ped_file"
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_check_PED_quad.py a_ped_file"
         raise SystemExit
 
diff --git a/NHS_WES_extract_shared_vars.py b/NHS_WES_extract_shared_vars.py
index 83e94aa20a398592d7fc9aca1cf5a04c4bd1e409..f75c695949303e45ab3329e3522a1cb4c39d0a07 100755
--- a/NHS_WES_extract_shared_vars.py
+++ b/NHS_WES_extract_shared_vars.py
@@ -126,6 +126,6 @@ if __name__ == '__main__':
     if len(sys.argv) == 4:
         go(sys.argv[1],sys.argv[2],sys.argv[3])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_extract_shared_vars.py in_vcf comma,sep,list,of,ids out_vcf"
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_extract_shared_vars.py in_vcf comma,sep,list,of,ids out_vcf"
         raise SystemExit
 
diff --git a/NHS_WES_extract_trio_FAM_PRO_ID.py b/NHS_WES_extract_trio_FAM_PRO_ID.py
index e936cc71a751440d70d9d620b2e20a2569a8ef08..c215a0119840b8839964a4fa3d770f81a0f20c0b 100755
--- a/NHS_WES_extract_trio_FAM_PRO_ID.py
+++ b/NHS_WES_extract_trio_FAM_PRO_ID.py
@@ -115,6 +115,6 @@ if __name__ == '__main__':
     if len(sys.argv) == 2:
         go(sys.argv[1])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_extract_trio_FAM_PRO_ID.py /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}"
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_extract_trio_FAM_PRO_ID.py /scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}"
         raise SystemExit
 
diff --git a/NHS_WES_generate_DEC_IGV.py b/NHS_WES_generate_DEC_IGV.py
index 0fdb863498ba8bbe4898a4113894bfc6e8862d42..95d204eacd86a269e79c37510f2756f3ce76c4c9 100755
--- a/NHS_WES_generate_DEC_IGV.py
+++ b/NHS_WES_generate_DEC_IGV.py
@@ -1395,7 +1395,7 @@ if __name__ == '__main__':
     if len(sys.argv) == 12:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],sys.argv[6],sys.argv[7],sys.argv[8],sys.argv[9],sys.argv[10],sys.argv[11])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_generate_DEC_IGV.py \
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_generate_DEC_IGV.py \
         dec_map_file,trans_map_file,ped_file,in_g2p_file,in_vase_file,fam_igv_dir,vcf_dir,plate_id,fam_id,dec_dir,fam_bam_dir"
         raise SystemExit
 
diff --git a/NHS_WES_generate_DEC_IGV.py.v1 b/NHS_WES_generate_DEC_IGV.py.v1
index 00a1e4d9664c72d1f81d9fbe5a9b3971aaf51cab..87c4c1d5451972193b849989271f464e9d7d2180 100755
--- a/NHS_WES_generate_DEC_IGV.py.v1
+++ b/NHS_WES_generate_DEC_IGV.py.v1
@@ -920,7 +920,7 @@ if __name__ == '__main__':
     if len(sys.argv) == 12:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],sys.argv[6],sys.argv[7],sys.argv[8],sys.argv[9],sys.argv[10],sys.argv[11])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_generate_DEC_IGV.py \
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_generate_DEC_IGV.py \
         dec_map_file,trans_map_file,ped_file,in_g2p_file,in_vase_file,fam_igv_dir,vcf_dir,plate_id,fam_id,dec_dir,fam_bam_dir"
         raise SystemExit
 
diff --git a/NHS_WES_generate_DEC_IGV.py_wrong_gene_trans b/NHS_WES_generate_DEC_IGV.py_wrong_gene_trans
index 3d08582cd939755fe442ca128c39fd68a3a5f754..7cbf1acc5bfa8a95a5e7fd5b4d211639e4a40471 100755
--- a/NHS_WES_generate_DEC_IGV.py_wrong_gene_trans
+++ b/NHS_WES_generate_DEC_IGV.py_wrong_gene_trans
@@ -1366,7 +1366,7 @@ if __name__ == '__main__':
     if len(sys.argv) == 12:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],sys.argv[6],sys.argv[7],sys.argv[8],sys.argv[9],sys.argv[10],sys.argv[11])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_generate_DEC_IGV.py \
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_generate_DEC_IGV.py \
         dec_map_file,trans_map_file,ped_file,in_g2p_file,in_vase_file,fam_igv_dir,vcf_dir,plate_id,fam_id,dec_dir,fam_bam_dir"
         raise SystemExit
 
diff --git a/NHS_WES_generate_DEC_IGV_aff_probands.py b/NHS_WES_generate_DEC_IGV_aff_probands.py
index 25a965b83bba82bb543a96375eacdeccc40c9e01..7014b2d3a6e8c2c16ec805af9ff681e93ae62ea8 100755
--- a/NHS_WES_generate_DEC_IGV_aff_probands.py
+++ b/NHS_WES_generate_DEC_IGV_aff_probands.py
@@ -535,7 +535,7 @@ if __name__ == '__main__':
     if len(sys.argv) == 11:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],sys.argv[6],sys.argv[7],sys.argv[8],sys.argv[9],sys.argv[10])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_generate_DEC_IGV_aff_probands.py \
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_generate_DEC_IGV_aff_probands.py \
         dec_id,trans_map_file,ped_file,in_g2p_file,fam_igv_dir,vcf_dir,plate_id,fam_id,dec_dir,fam_bam_dir"
         raise SystemExit
 
diff --git a/NHS_WES_generate_DEC_IGV_sib_from_quad.py b/NHS_WES_generate_DEC_IGV_sib_from_quad.py
index eb978f20ef453440264bdbcaca17263b83914aa8..2946a2d02219934a3afa437c4541de23eae0bad9 100755
--- a/NHS_WES_generate_DEC_IGV_sib_from_quad.py
+++ b/NHS_WES_generate_DEC_IGV_sib_from_quad.py
@@ -541,7 +541,7 @@ if __name__ == '__main__':
     if len(sys.argv) == 11:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],sys.argv[6],sys.argv[7],sys.argv[8],sys.argv[9],sys.argv[10])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_generate_DEC_IGV_aff_probands.py \
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_generate_DEC_IGV_aff_probands.py \
         dec_id,trans_map_file,ped_file,in_g2p_file,fam_igv_dir,vcf_dir,plate_id,fam_id,dec_dir,fam_bam_dir"
         raise SystemExit
 
diff --git a/NHS_WES_generate_DEC_IGV_trio_from_quad.py b/NHS_WES_generate_DEC_IGV_trio_from_quad.py
index 6b9e2d1a01d956f60a204903c74474a2de8180e9..33462d2a8ffa235d1f116d292ceeb96c81a9bb7f 100755
--- a/NHS_WES_generate_DEC_IGV_trio_from_quad.py
+++ b/NHS_WES_generate_DEC_IGV_trio_from_quad.py
@@ -1397,7 +1397,7 @@ if __name__ == '__main__':
     if len(sys.argv) == 13:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],sys.argv[6],sys.argv[7],sys.argv[8],sys.argv[9],sys.argv[10],sys.argv[11],sys.argv[12])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/NHS_WES_generate_DEC_IGV.py \
+        print "Suggested use: time python /home/u035/u035/shared/scripts/NHS_WES_generate_DEC_IGV.py \
         dec_map_file,trans_map_file,ped_file,in_g2p_file,in_vase_file,fam_igv_dir,vcf_dir,plate_id,fam_id,dec_dir,fam_bam_dir,indi_id_for_this_kid"
         raise SystemExit
 
diff --git a/NHS_WES_generate_aff_sib_ped.py b/NHS_WES_generate_aff_sib_ped.py
index 17b5b309e1488019b6ca5ba50beba22f8d48c1ed..4158999d7d81da69e662ca53c2ac68abcce30875 100644
--- a/NHS_WES_generate_aff_sib_ped.py
+++ b/NHS_WES_generate_aff_sib_ped.py
@@ -43,6 +43,6 @@ if __name__ == '__main__':
     if len(sys.argv) == 5:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4])
     else:
-        print "Suggested use: time $PYTHON /home/u035/project/scripts/NHS_WES_generate_aff_sib_ped.py ${PED_DIR} ${quad_ped_file} ${KID_1_ID} ${KID_2_ID}"
+        print "Suggested use: time $PYTHON /home/u035/u035/shared/scripts/NHS_WES_generate_aff_sib_ped.py ${PED_DIR} ${quad_ped_file} ${KID_1_ID} ${KID_2_ID}"
         raise SystemExit
 
diff --git a/NHS_WES_generate_coverage_result_file.py b/NHS_WES_generate_coverage_result_file.py
index 8c20a01710f6e4d7a79ee3a1117ae9a342601e94..6bd2d6a38181f8c011684f9f0b5aa574cdd8c40c 100644
--- a/NHS_WES_generate_coverage_result_file.py
+++ b/NHS_WES_generate_coverage_result_file.py
@@ -114,9 +114,9 @@ if __name__ == '__main__':
     if len(sys.argv) == 4:
         go(sys.argv[1],sys.argv[2],sys.argv[3])
     else:
-        print "Suggested use: time $PYTHON /home/u035/project/scripts/generate_coverage_result_file.py \
+        print "Suggested use: time $PYTHON /home/u035/u035/shared/scripts/generate_coverage_result_file.py \
                               DDG2P.s14-NFE-Twist-NA12878.sample_interval_summary \
-                              /home/u035/project/resources/DDG2P.20180830.ClinVar.20190520.plus15bp.txt \
+                              /home/u035/u035/shared/resources/G2P/DDG2P.20180830.ClinVar.20190520.plus15bp.txt \
                               DDG2P.s14-NFE-Twist-NA12878.COV.txt"
         raise SystemExit
 
diff --git a/NHS_WES_generate_trio_VCF.py b/NHS_WES_generate_trio_VCF.py
index 7d5425d4506610c6a07d9aa65146b4994c1071b7..d856ded0e3c0a32cea5aa533b2fabed68cdc5a81 100644
--- a/NHS_WES_generate_trio_VCF.py
+++ b/NHS_WES_generate_trio_VCF.py
@@ -42,6 +42,6 @@ if __name__ == '__main__':
     if len(sys.argv) == 6:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5])
     else:
-        print "Suggested use: time $PYTHON /home/u035/project/scripts/NHS_WES_generate_trio_ped.py ${PED_DIR} ${quad_ped_file} ${KID_ID} ${PAR_1_ID} ${PAR_2_ID}"
+        print "Suggested use: time $PYTHON /home/u035/u035/shared/scripts/NHS_WES_generate_trio_ped.py ${PED_DIR} ${quad_ped_file} ${KID_ID} ${PAR_1_ID} ${PAR_2_ID}"
         raise SystemExit
 
diff --git a/NHS_WES_generate_trio_ped.py b/NHS_WES_generate_trio_ped.py
index 9ea04f2c3a1ee0b2d66e220075e2dba30e32e10c..bd7d0bf6328978802fce15a8c52e221c250fcdf3 100644
--- a/NHS_WES_generate_trio_ped.py
+++ b/NHS_WES_generate_trio_ped.py
@@ -42,6 +42,6 @@ if __name__ == '__main__':
     if len(sys.argv) == 6:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5])
     else:
-        print "Suggested use: time $PYTHON /home/u035/project/scripts/NHS_WES_generate_trio_ped.py ${PED_DIR} ${quad_ped_file} ${KID_ID} ${PAR_1_ID} ${PAR_2_ID}"
+        print "Suggested use: time $PYTHON /home/u035/u035/shared/scripts/NHS_WES_generate_trio_ped.py ${PED_DIR} ${quad_ped_file} ${KID_ID} ${PAR_1_ID} ${PAR_2_ID}"
         raise SystemExit
 
diff --git a/NHS_WES_trio_cram_setup.sh b/NHS_WES_trio_cram_setup.sh
index c8f5f4544067304a4da542b1b29d9d8b4fe94dba..a8cc30d0cb9d05feefa4b16370a9ab0d5d2cfd7c 100755
--- a/NHS_WES_trio_cram_setup.sh
+++ b/NHS_WES_trio_cram_setup.sh
@@ -7,7 +7,7 @@
 
 
 ### Setup the folder structure for the downstream analysis###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -19,14 +19,14 @@ DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
 BAMOUT_DIR=${WORK_DIR}/BAMOUT
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 ### Tools
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-SAMTOOLS=/home/u035/project/software/bcbio/anaconda/bin/samtools
-PICARD=/home/u035/project/software/bcbio/anaconda/bin/picard
-REFERENCE_GENOME=/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+SAMTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/bin/samtools
+PICARD=/home/u035/u035/shared/software/bcbio/anaconda/bin/picard
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 # check if ${WORK_DIR} already exists - if so, exit - to prevent accidental overwriting
@@ -38,7 +38,7 @@ fi
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"	# the general path to the source VCF, BAM and PED files			i.e. /scratch/u035/project/trio_whole_exome/analysis/output
+echo "SOURCE_DIR = ${SOURCE_DIR}"	# the general path to the source VCF, BAM and PED files			i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output
 echo "BATCH_ID = ${BATCH_ID}"		# the ID of the batch being processed 					e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}" 		# the PCR plate ID of the batch being currently processed, 		e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"	# this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
diff --git a/NHS_WES_trio_delete_BAM.sh b/NHS_WES_trio_delete_BAM.sh
index 5bd4af7deec17ecb4b5efad8739635d4cef46b23..5fb4a5f788d26cacd47b353a43a3e1e2e61075ad 100755
--- a/NHS_WES_trio_delete_BAM.sh
+++ b/NHS_WES_trio_delete_BAM.sh
@@ -7,7 +7,7 @@
 
 
 ### Setup the folder structure for the downstream analysis###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -19,10 +19,10 @@ DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
 BAMOUT_DIR=${WORK_DIR}/BAMOUT
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"	# the general path to the source VCF, BAM and PED files			i.e. /scratch/u035/project/trio_whole_exome/analysis/output/${VERSION_N}_${PLATE_ID}
+echo "SOURCE_DIR = ${SOURCE_DIR}"	# the general path to the source VCF, BAM and PED files			i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/${VERSION_N}_${PLATE_ID}
 echo "BATCH_ID = ${BATCH_ID}"		# the ID of the batch being processed 					e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}" 		# the PCR plate ID of the batch being currently processed, 		e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"	# this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
diff --git a/NHS_WES_trio_setup.sh b/NHS_WES_trio_setup.sh
index 891a20280db6b6acdd7b7778da63eb03ed9c9894..f82d34a4f1d9b8c35b16c1f61ac05b372de9cd73 100755
--- a/NHS_WES_trio_setup.sh
+++ b/NHS_WES_trio_setup.sh
@@ -7,7 +7,7 @@
 
 
 ### Setup the folder structure for the downstream analysis###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -19,11 +19,11 @@ DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
 BAMOUT_DIR=${WORK_DIR}/BAMOUT
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 ### Tools
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
 
 
 
@@ -36,7 +36,7 @@ fi
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"	# the general path to the source VCF, BAM and PED files			i.e. /scratch/u035/project/trio_whole_exome/analysis/output
+echo "SOURCE_DIR = ${SOURCE_DIR}"	# the general path to the source VCF, BAM and PED files			i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output
 echo "BATCH_ID = ${BATCH_ID}"		# the ID of the batch being processed 					e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}" 		# the PCR plate ID of the batch being currently processed, 		e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"	# this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
diff --git a/bcbio_gnomad_install.sh b/bcbio_gnomad_install.sh
index 13563b6a751c400113a83ae4021d2d8a27cf07db..705f1a5811689d4fe7360ab2eade85237e709679 100755
--- a/bcbio_gnomad_install.sh
+++ b/bcbio_gnomad_install.sh
@@ -5,9 +5,9 @@
 #PBS -N bcbio_gnomad_install
 #PBS -j oe
 
-cd /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/txtmp
+cd /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/txtmp
 
-PATH=$PATH:/home/u035/project/software/bcbio/anaconda/bin
+PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/bin
 
 ref=../seq/hg38.fa
 fields_to_keep="INFO/"$(cat gnomad_fields_to_keep.txt | paste -s | sed s/"\t"/",INFO\/"/g)
diff --git a/decipher_NHS_WES_trio.sh b/decipher_NHS_WES_trio.sh
index a185044e8bf51c4bb51a9f4df87fbe3c4f5d2dc8..ee7210c279d852e276ec400b299d308914c87fac 100755
--- a/decipher_NHS_WES_trio.sh
+++ b/decipher_NHS_WES_trio.sh
@@ -7,13 +7,13 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
-#BASE=/scratch/u035/project/analysis/wes_pilot
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+#BASE=/scratch/u035/u035/shared/analysis/wes_pilot
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -24,36 +24,36 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 
 # other files to be used
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt							# created by NHS_WES_trio_setup.sh
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt							# created by NHS_WES_trio_setup.sh
-TARGETS=/home/u035/project/resources/DDG2P.20190919.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt				# OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt				# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt			# OK
+TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt			# OK
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
-REFERENCE_GENOME=/home/u035/project/data/reference/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
+echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/
 echo "BATCH_ID = ${BATCH_ID}"           # the ID of the batch being processed                                   	e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}"           # the PCR plate ID of the batch being currently processed,              	e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"       # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
diff --git a/download_gnomADg.sh b/download_gnomADg.sh
deleted file mode 100755
index a5a54e9e84cc83af11504e8017ae91758eccd575..0000000000000000000000000000000000000000
--- a/download_gnomADg.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-#PBS -l walltime=48:00:00
-#PBS -l ncpus=1,mem=2gb
-#PBS -q uv2000
-#PBS -N download_gnomADg
-#PBS -j oe
-
-
-DATA_DIR=/home/u035/project/resources/gnomad/r2.1/genomes
-
-cd ${DATA_DIR}
-
-wget ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad/r2.1/genomes/*.gz
-wget ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad/r2.1/genomes/*.tbi
-
diff --git a/downstream_setup.sh b/downstream_setup.sh
index d610ebb41b8b75452e7dc3d0dd0dfe1e78059970..fa25954fbd3b834e9a896384740229e6a6599855 100755
--- a/downstream_setup.sh
+++ b/downstream_setup.sh
@@ -7,7 +7,7 @@
 
 
 ### Setup the folder structure for the downstream analysis###
-BASE=/scratch/u035/project/analysis/wes_pilot
+BASE=/scratch/u035/u035/shared/analysis/wes_pilot
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -18,10 +18,10 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 ### Tools
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
 
 
 
diff --git a/extract_BED_CCDS_DDG2P.py b/extract_BED_CCDS_DDG2P.py
index e12ab94c2364d67560fec908647756a8eb9773b8..33e1e11be76a4bced5af681a39f3788788d1fa05 100644
--- a/extract_BED_CCDS_DDG2P.py
+++ b/extract_BED_CCDS_DDG2P.py
@@ -1,6 +1,6 @@
 #	given 
-#		the BED file for all genes (/home/u035/project/resources/CCDS.20180614.plus15bp.merged.bed)
-#		and the file for the genes in the DDG2P (unique gene names, inluding synonyms, i.e., /home/u035/project/resources/genes_in_DDG2P.30082018.txt)
+#		the BED file for all genes (/home/u035/u035/shared/resources/exome_targets/CCDS.20180614.plus15bp.merged.bed)
+#		and the file for the genes in the DDG2P (unique gene names, inluding synonyms, i.e., /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.30082018.txt)
 #	extract 
 #		the BED file for the DDG2P genes
 #
diff --git a/extract_trio_FAM_PRO_ID.py b/extract_trio_FAM_PRO_ID.py
index e58c60acd0e2cb1661e4a8359c16e68e3f957ead..e66d8f4cef2867cc6ffabc94881ea97abcc58d60 100755
--- a/extract_trio_FAM_PRO_ID.py
+++ b/extract_trio_FAM_PRO_ID.py
@@ -111,6 +111,6 @@ if __name__ == '__main__':
     if len(sys.argv) == 2:
         go(sys.argv[1])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/extract_trio_FAM_PRO_ID.py /scratch/u035/project/analysis/wes_pilot/03062019"
+        print "Suggested use: time python /home/u035/u035/shared/scripts/extract_trio_FAM_PRO_ID.py /scratch/u035/u035/shared/analysis/wes_pilot/03062019"
         raise SystemExit
 
diff --git a/full_process_NHS_WES_trio.sh b/full_process_NHS_WES_trio.sh
index 38fd7b924be43d72674de8964973f0a8c0399a10..f2bc21eb8e893cf15c916f0575a0cfddf17d302a 100755
--- a/full_process_NHS_WES_trio.sh
+++ b/full_process_NHS_WES_trio.sh
@@ -7,13 +7,13 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
-#BASE=/scratch/u035/project/analysis/wes_pilot
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+#BASE=/scratch/u035/u035/shared/analysis/wes_pilot
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -24,36 +24,36 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 
 # other files to be used
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt							# created by NHS_WES_trio_setup.sh
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt							# created by NHS_WES_trio_setup.sh
-TARGETS=/home/u035/project/resources/DDG2P.20190919.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt				# OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt				# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt			# OK
+TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt			# OK
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
-REFERENCE_GENOME=/home/u035/project/data/reference/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
+echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/
 echo "BATCH_ID = ${BATCH_ID}"           # the ID of the batch being processed                                   	e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}"           # the PCR plate ID of the batch being currently processed,              	e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"       # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
@@ -153,7 +153,7 @@ G2P_LOG_DIR=${G2P_DIR}/${FAMILY_ID}_LOG_DIR
 mkdir ${G2P_LOG_DIR}
 TXT_OUT=${G2P_LOG_DIR}/${FAMILY_ID}.report.txt
 HTML_OUT=${G2P_LOG_DIR}/${FAMILY_ID}.report.html
-VCF_KEYS='gnomADe|gnomADg'
+VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
 
 
 time ${VEP} \
@@ -166,11 +166,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 97 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.19092019.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-97.3-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.19092019.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.19092019.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-97.3-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.19092019.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',
 af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 echo ""
@@ -225,7 +225,7 @@ cd ${VASE_DIR}
 time ${GATK4} IndexFeatureFile -F ${OUT_FILE}
 
 # select only variants on the 24 chromosomes
-time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/project/resources/24_chr.list --exclude-non-variants
+time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/u035/shared/resources/24_chr.list --exclude-non-variants
 
 # sort the VCF (maybe not needed?, but just in case, and it is quick)
 rm ${FAMILY_ID}.strict.24chr.sort.denovo.vcf
diff --git a/gather_NHS_WES_aff_probands_results.sh b/gather_NHS_WES_aff_probands_results.sh
index 8576ca793cdb65aabe4193b5b433516bfd11677a..01b6f99f09ddd5b1f404081a4e9acd38d22c90bb 100755
--- a/gather_NHS_WES_aff_probands_results.sh
+++ b/gather_NHS_WES_aff_probands_results.sh
@@ -8,7 +8,7 @@
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=${BASE}/${PROJECT_ID}
 NHS_DIR=${WORK_DIR}/${PLATE_ID}_${VERSION_N}_results
 
diff --git a/gather_NHS_WES_quad_results.sh b/gather_NHS_WES_quad_results.sh
index a89d093c4c0dda93c772c56bae411c25e154a05d..f619b11ce43b7b942b379c60ccb50ba2a5464467 100755
--- a/gather_NHS_WES_quad_results.sh
+++ b/gather_NHS_WES_quad_results.sh
@@ -8,7 +8,7 @@
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=${BASE}/${PROJECT_ID}
 NHS_DIR=${WORK_DIR}/${PLATE_ID}_${VERSION_N}_results
 
diff --git a/gather_NHS_WES_trio_results.sh b/gather_NHS_WES_trio_results.sh
index 6ff0dd1c32385bea699e225e0a8cbc1e9c36e609..59379f6631a4c01703bb86988984dc688b64ce4d 100755
--- a/gather_NHS_WES_trio_results.sh
+++ b/gather_NHS_WES_trio_results.sh
@@ -8,7 +8,7 @@
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=${BASE}/${PROJECT_ID}
 NHS_DIR=${WORK_DIR}/${PLATE_ID}_${VERSION_N}_results
 
diff --git a/generate_DEC_IGV.py b/generate_DEC_IGV.py
index e293d2ce7de8bfb841833958b920410747fc60c0..21b24f168da0208afedcc4c214e548eaf5b8111a 100755
--- a/generate_DEC_IGV.py
+++ b/generate_DEC_IGV.py
@@ -942,10 +942,10 @@ if __name__ == '__main__':
     if len(sys.argv) == 12:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],sys.argv[6],sys.argv[7],sys.argv[8],sys.argv[9],sys.argv[10],sys.argv[11])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/generate_DEC_IGV.py \
+        print "Suggested use: time python /home/u035/u035/shared/scripts/generate_DEC_IGV.py \
         2820-gatk-haplotype-annotated.2820_2820.vcf.gz \
         ../output_dd/2820_log_dir/2820.report.txt \
-        /scratch/u035/project/analysis/wes_pilot/VASE/08042019/output/2820_2820.strict.denovo.vcf \
+        /scratch/u035/u035/shared/analysis/wes_pilot/VASE/08042019/output/2820_2820.strict.denovo.vcf \
         2820_2820 \
         2820_2820.DEC.txt \
         DECIPHER_DIR \
diff --git a/generate_G2P_out_VCF.py b/generate_G2P_out_VCF.py
index cfae641c0934b9d33c4b7986987cb508a24f80fa..b178d0a722a3943b0222672d26897e0554d82825 100755
--- a/generate_G2P_out_VCF.py
+++ b/generate_G2P_out_VCF.py
@@ -166,7 +166,7 @@ if __name__ == '__main__':
     if len(sys.argv) == 5:
         go(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4])
     else:
-        print "Suggested use: time python /home/u035/project/scripts/generate_G2P_out_VCF.py 2820-gatk-haplotype-annotated.2820_2820.vcf.gz ../output_dd/2820_log_dir/2820.report.txt 2820_2820 2820_2820.G2P.vcf "
+        print "Suggested use: time python /home/u035/u035/shared/scripts/generate_G2P_out_VCF.py 2820-gatk-haplotype-annotated.2820_2820.vcf.gz ../output_dd/2820_log_dir/2820.report.txt 2820_2820 2820_2820.G2P.vcf "
         raise SystemExit
 
 
diff --git a/generate_coverage_result_file.py b/generate_coverage_result_file.py
index 50e8c6f03675390324ad102d5ac0440a2700503d..ba8712e46d4aaa413eb61c125504f53c9bffa0a8 100644
--- a/generate_coverage_result_file.py
+++ b/generate_coverage_result_file.py
@@ -114,9 +114,9 @@ if __name__ == '__main__':
     if len(sys.argv) == 4:
         go(sys.argv[1],sys.argv[2],sys.argv[3])
     else:
-        print "Suggested use: time $PYTHON /home/u035/project/scripts/generate_coverage_result_file.py \
+        print "Suggested use: time $PYTHON /home/u035/u035/shared/scripts/generate_coverage_result_file.py \
                               DDG2P.s14-NFE-Twist-NA12878.sample_interval_summary \
-                              /home/u035/project/resources/DDG2P.20180830.ClinVar.20190520.plus15bp.txt \
+                              /home/u035/u035/shared/resources/G2P/DDG2P.20180830.ClinVar.20190520.plus15bp.txt \
                               DDG2P.s14-NFE-Twist-NA12878.COV.txt"
         raise SystemExit
 
diff --git a/old_downstream_setup.sh b/old_downstream_setup.sh
index b29e00b969cbc7c6b53157a5ff49d4f4ef77de79..1c8806b16483b7aeb30702f0b5d2dbb82e8fda10 100755
--- a/old_downstream_setup.sh
+++ b/old_downstream_setup.sh
@@ -13,9 +13,9 @@ DATE_BATCH=${DATE}_${BATCH}
 echo "DATE_BATCH = ${DATE_BATCH}"
 
 
-BASE=/scratch/u035/project/analysis/wes_pilot
-SOURCE_DIR=/scratch/u035/project/analysis/wes_pilot/bcbio/final
-PED_DIR=/scratch/u035/project/analysis/wes_pilot/params 
+BASE=/scratch/u035/u035/shared/analysis/wes_pilot
+SOURCE_DIR=/scratch/u035/u035/shared/analysis/wes_pilot/bcbio/final
+PED_DIR=/scratch/u035/u035/shared/analysis/wes_pilot/params 
 
 
 WORK_DIR=$BASE/${PROJECT_ID}
@@ -24,9 +24,9 @@ VASE_DIR=${WORK_DIR}/VASE
 COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
 
 
 # create the working dir and the required subfolders
diff --git a/old_submit_downstream.sh b/old_submit_downstream.sh
index 18b4e94cbcdb224472c012c530487a32444ddc5c..9b52a3d641d96bd99519dc854a4e54d291a64423 100755
--- a/old_submit_downstream.sh
+++ b/old_submit_downstream.sh
@@ -14,15 +14,15 @@ echo "DATE_BATCH = ${DATE_BATCH}"
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 # where the VCF and BAM files are after the alignemnt and variant calling steps
-SOURCE_DIR=/scratch/u035/project/analysis/wes_pilot/bcbio/final
+SOURCE_DIR=/scratch/u035/u035/shared/analysis/wes_pilot/bcbio/final
 
 
-BASE=/scratch/u035/project/analysis/wes_pilot
+BASE=/scratch/u035/u035/shared/analysis/wes_pilot
 WORK_DIR=$BASE/${PROJECT_ID}
 G2P_DIR=${WORK_DIR}/G2P
 VASE_DIR=${WORK_DIR}/VASE 
@@ -33,28 +33,28 @@ CNV_DIR=${WORK_DIR}/CNV
 LOG_DIR=${WORK_DIR}/LOG
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt
 
 
-TARGETS=/home/u035/project/resources/DDG2P.20180830.plus15bp.merged.bed
-CLINVAR=/home/u035/project/resources/DDG2P.20180830.clinvar.20190603.plus15bp.txt
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20180830.plus15bp.merged.bed
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20180830.clinvar.20190603.plus15bp.txt
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"
-REFERENCE_GENOME=/home/u035/project/data/reference/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
@@ -158,11 +158,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 96 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.30082018.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-96.0-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.30082018.csv',af_from_vcf=1,log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.30082018.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-96.0-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.30082018.csv',af_from_vcf=1,log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 echo ""
 echo ""
@@ -212,7 +212,7 @@ cd ${VASE_DIR}
 time ${GATK4} IndexFeatureFile -F ${OUT_FILE}
 
 # select only variants on the 24 chromosomes
-time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/project/resources/24_chr.list --exclude-non-variants
+time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/u035/shared/resources/24_chr.list --exclude-non-variants
 
 # sort the VCF (maybe not needed?, but just in case, and it is quick)
 rm ${FAMILY_ID}.strict.24chr.sort.denovo.vcf
@@ -224,7 +224,7 @@ time ${GATK4} IndexFeatureFile -F ${FAMILY_ID}.strict.24chr.sort.denovo.vcf
 
 # remove variants from LCR and telo-/centro-mere regions
 time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${FAMILY_ID}.strict.24chr.sort.denovo.vcf -O ${FAMILY_ID}.clean.denovo.vcf \
--XL /home/u035/project/resources/LCR.bed -XL /home/u035/project/resources/sv_repeat_telomere_centromere.bed --exclude-non-variants
+-XL /home/u035/u035/shared/resources/LCR.bed -XL /home/u035/u035/shared/resources/sv_repeat_telomere_centromere.bed --exclude-non-variants
 
 # split multi-allelic sites [by -m -any]
 # left-alignment and normalization [by adding the -f]
diff --git a/old_submit_trio_wes_aspera_download.sh b/old_submit_trio_wes_aspera_download.sh
index 2a1221a0efc34bd5a7ecae4172424f34b30f1376..776b53f6da668eec350e4d121372d8a6bb6ab78c 100755
--- a/old_submit_trio_wes_aspera_download.sh
+++ b/old_submit_trio_wes_aspera_download.sh
@@ -7,12 +7,12 @@
 
 source $TRANSFER_INFO_FILE
 
-/home/u035/project/software/aspera/connect/bin/ascp \
+/home/u035/u035/shared/software/aspera/connect/bin/ascp \
   -T -P 33001 -O 33001 -l 500M -k2 --overwrite=diff \
   $ASPERA_SCP_USER@transfer.genomics.ed.ac.uk:$PROJECT \
-  /scratch/u035/project/trio_whole_exome/data
+  /scratch/u035/u035/shared/trio_whole_exome/data
 
-cd /scratch/u035/project/trio_whole_exome/data/$PROJECT/raw_data
+cd /scratch/u035/u035/shared/trio_whole_exome/data/$PROJECT/raw_data
 
 rm ../md5_check.txt 2> /dev/null
 for DATE in 20*[0-9]
diff --git a/process_NHS_WES_aff_probands.sh b/process_NHS_WES_aff_probands.sh
index 3afbfa1bedc001209aa6c6944723cf6603d6221e..7cb0c832035ed2c93f20bd628b3a1494ebfbe39a 100755
--- a/process_NHS_WES_aff_probands.sh
+++ b/process_NHS_WES_aff_probands.sh
@@ -7,13 +7,13 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh, done previously by the stanard trio-based pipeline ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -25,37 +25,37 @@ DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
 BAMOUT_DIR=${WORK_DIR}/BAMOUT
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 
 # other files to be used
-TARGETS=/home/u035/project/resources/DDG2P.20210706.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20210706.clinvar.20210626.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt				# OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt				# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20210706.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20210706.clinvar.20210626.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt			# OK
+TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt			# OK
 
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk							# points to ../share/gatk4-4.1.8.1-0/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON3=/home/u035/project/software/bcbio/anaconda/bin/python3							# points to python3.6
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-100.4-0/vep
-REFERENCE_GENOME=/home/u035/project/resources/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk							# points to ../share/gatk4-4.1.8.1-0/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON3=/home/u035/u035/shared/software/bcbio/anaconda/bin/python3							# points to python3.6
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-100.4-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
+echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/
 echo "BATCH_ID = ${BATCH_ID}"           # the ID of the batch being processed                                   	e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}"           # the PCR plate ID of the batch being currently processed,              	e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"       # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
@@ -165,7 +165,7 @@ mkdir ${G2P_LOG_DIR}
 TXT_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}.report.txt
 HTML_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}.report.html
 #VCF_KEYS='gnomADe|gnomADg'     # old VEP version 97
-VCF_KEYS='gnomADe_GRCh38|gnomADg_r3.0_GRCh38'
+VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
 
 
 time ${VEP} \
@@ -178,11 +178,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 100 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20210706.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.20210706.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 
 echo ""
@@ -437,7 +437,7 @@ done
 
 ##############################################################################################
 ## write the IGV batch file for each affected individual in this family based on the bamouts #
-## to be stored as /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.snapshot.txt #
+## to be stored as /scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.snapshot.txt #
 ## ${PROBAND_ID}_${FAMILY_ID} == ${aff_pro_arr[$key] #
 ##################################################################
 
@@ -446,7 +446,7 @@ for key in "${!aff_pro_arr[@]}"; do
   echo "" 
   echo "Generating the IGV batch file for ${aff_pro_arr[$key]}";
 
-  snap_file=/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${aff_pro_arr[$key]}.snapshot.txt
+  snap_file=/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${aff_pro_arr[$key]}.snapshot.txt
 
   # check if previous version exist, if so - delete it
   if [ -f "${snap_file}" ]; then
@@ -457,7 +457,7 @@ for key in "${!aff_pro_arr[@]}"; do
   # write the header for the IGV batch file
   echo "new" >> ${snap_file}
   echo "genome hg38" >> ${snap_file}
-  echo "snapshotDirectory \"/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}\"" >> ${snap_file}
+  echo "snapshotDirectory \"/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}\"" >> ${snap_file}
   echo "" >> ${snap_file}
 
 
diff --git a/process_NHS_WES_quad.sh b/process_NHS_WES_quad.sh
index 87076ef01d500e94037f0938b34baad02f5e6d7a..da99c05c40394fd319dbdb03f93568b0d994f0ca 100755
--- a/process_NHS_WES_quad.sh
+++ b/process_NHS_WES_quad.sh
@@ -7,13 +7,13 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh, done previously by the stanard trio-based pipeline ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -25,37 +25,37 @@ DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
 BAMOUT_DIR=${WORK_DIR}/BAMOUT
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 
 # other files to be used
-TARGETS=/home/u035/project/resources/DDG2P.20210706.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20210706.clinvar.20210626.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt				# OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt				# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20210706.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20210706.clinvar.20210626.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt			# OK
+TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt			# OK
 
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk							# points to ../share/gatk4-4.1.8.1-0/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON3=/home/u035/project/software/bcbio/anaconda/bin/python3							# points to python3.6
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-100.4-0/vep
-REFERENCE_GENOME=/home/u035/project/resources/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk							# points to ../share/gatk4-4.1.8.1-0/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON3=/home/u035/u035/shared/software/bcbio/anaconda/bin/python3							# points to python3.6
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-100.4-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
+echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/
 echo "BATCH_ID = ${BATCH_ID}"           # the ID of the batch being processed                                   	e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}"           # the PCR plate ID of the batch being currently processed,              	e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"       # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
@@ -217,7 +217,7 @@ for KID_ID in ${KID_IDS[@]}; do
     mkdir ${G2P_LOG_DIR}
     TXT_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.report.txt
     HTML_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_${KID_ID}.report.html
-    VCF_KEYS='gnomADe_GRCh38|gnomADg_r3.0_GRCh38'
+    VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
 
     time ${VEP} \
         -i ${IN_FILE} \
@@ -229,11 +229,11 @@ for KID_ID in ${KID_IDS[@]}; do
         --merged \
         --use_given_ref \
         --cache --cache_version 100 \
-        --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+        --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
         --individual all \
-        --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20210706.txt" \
-        --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
-        --plugin G2P,file='/home/u035/project/resources/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+        --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.20210706.txt" \
+        --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
+        --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
     echo ""
     echo ""
@@ -284,7 +284,7 @@ for KID_ID in ${KID_IDS[@]}; do
     time ${GATK4} IndexFeatureFile -I ${OUT_FILE}
 
     # select only variants on the 24 chromosomes
-    time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.denovo.vcf -L /home/u035/project/resources/24_chr.list --exclude-non-variants
+    time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.denovo.vcf -L /home/u035/u035/shared/resources/24_chr.list --exclude-non-variants
 
     # sort the VCF (maybe not needed?, but just in case, and it is quick)
     rm ${PLATE_ID}_${FAMILY_ID}_${KID_ID}.strict.24chr.sort.denovo.vcf
@@ -488,10 +488,10 @@ for KID_ID in ${KID_IDS[@]}; do
 
     #################################################################
     # write the IGV batch file for this family based on the bamouts #
-    # to be stored as /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${KID_ID}_${FAMILY_ID}.snapshot.txt #
+    # to be stored as /scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${KID_ID}_${FAMILY_ID}.snapshot.txt #
     #################################################################
 
-    snap_file=/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${KID_ID}_${FAMILY_ID}.snapshot.txt
+    snap_file=/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${KID_ID}_${FAMILY_ID}.snapshot.txt
 
     # check if previous version exist, if so - delete it
     if [ -f "${snap_file}" ]; then
@@ -502,7 +502,7 @@ for KID_ID in ${KID_IDS[@]}; do
     # write the header for the IGV batch file
     echo "new" >> ${snap_file}
     echo "genome hg38" >> ${snap_file}
-    echo "snapshotDirectory \"/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}_${KID_ID}\"" >> ${snap_file}
+    echo "snapshotDirectory \"/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}_${KID_ID}\"" >> ${snap_file}
     echo "" >> ${snap_file}
 
     # now, go again over the variants in the DECIPHER file and generate one snapshot file for all the variants
@@ -680,7 +680,7 @@ G2P_LOG_DIR=${G2P_DIR}/${PLATE_ID}_${FAMILY_ID}_shared_LOG_DIR
 mkdir ${G2P_LOG_DIR}
 TXT_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.report.txt
 HTML_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}_shared.report.html
-VCF_KEYS='gnomADe_GRCh38|gnomADg_r3.0_GRCh38'
+VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
 
 time ${VEP} \
     -i ${IN_FILE} \
@@ -692,11 +692,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 100 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20210706.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.20210706.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 
 echo ""
@@ -877,7 +877,7 @@ done
 
 ##############################################################################################
 ## write the IGV batch file for each affected individual in this family based on the bamouts #
-## to be stored as /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.shared.snapshot.txt #
+## to be stored as /scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.shared.snapshot.txt #
 ## ${PROBAND_ID}_${FAMILY_ID} == ${aff_pro_arr[$key] #
 ##################################################################
 
@@ -886,7 +886,7 @@ for key in "${!aff_pro_arr[@]}"; do
   echo ""
   echo "Generating the IGV batch file for ${aff_pro_arr[$key]}";
 
-  snap_file=/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${aff_pro_arr[$key]}.shared.snapshot.txt
+  snap_file=/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${aff_pro_arr[$key]}.shared.snapshot.txt
 
   # check if previous version exist, if so - delete it
   if [ -f "${snap_file}" ]; then
@@ -898,7 +898,7 @@ for key in "${!aff_pro_arr[@]}"; do
   # write the header for the IGV batch file
   echo "new" >> ${snap_file}
   echo "genome hg38" >> ${snap_file}
-  echo "snapshotDirectory \"/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}_shared\"" >> ${snap_file}
+  echo "snapshotDirectory \"/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}_shared\"" >> ${snap_file}
   echo "" >> ${snap_file}
 
 
diff --git a/process_NHS_WES_quad_full.sh b/process_NHS_WES_quad_full.sh
index 9de198d410c97f88c56809257f46d71560dfc3fa..d56865541e228c6642f2c821d299a4ed72db1e68 100755
--- a/process_NHS_WES_quad_full.sh
+++ b/process_NHS_WES_quad_full.sh
@@ -7,13 +7,13 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh, done previously by the stanard trio-based pipeline ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -25,37 +25,37 @@ DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
 BAMOUT_DIR=${WORK_DIR}/BAMOUT
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 
 # other files to be used
-TARGETS=/home/u035/project/resources/DDG2P.20200601.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20200601.clinvar.20200520.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt				# OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt				# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20200601.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20200601.clinvar.20200520.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt			# OK
+TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt			# OK
 
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk							# points to ../share/gatk4-4.1.8.1-0/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON3=/home/u035/project/software/bcbio/anaconda/bin/python3							# points to python3.6
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-100.4-0/vep
-REFERENCE_GENOME=/home/u035/project/resources/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk							# points to ../share/gatk4-4.1.8.1-0/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON3=/home/u035/u035/shared/software/bcbio/anaconda/bin/python3							# points to python3.6
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-100.4-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
+echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/
 echo "BATCH_ID = ${BATCH_ID}"           # the ID of the batch being processed                                   	e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}"           # the PCR plate ID of the batch being currently processed,              	e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"       # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
@@ -166,7 +166,7 @@ mkdir ${G2P_LOG_DIR}
 TXT_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}.report.txt
 HTML_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}.report.html
 #VCF_KEYS='gnomADe|gnomADg'     # old VEP version 97
-VCF_KEYS='gnomADe_GRCh38|gnomADg_r3.0_GRCh38'
+VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
 
 
 time ${VEP} \
@@ -179,11 +179,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 100 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.01062020.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.01062020.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.01062020.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.01062020.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 
 echo ""
@@ -437,7 +437,7 @@ done
 
 ##############################################################################################
 ## write the IGV batch file for each affected individual in this family based on the bamouts #
-## to be stored as /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.snapshot.txt #
+## to be stored as /scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.snapshot.txt #
 ## ${PROBAND_ID}_${FAMILY_ID} == ${aff_pro_arr[$key] #
 ##################################################################
 
@@ -446,7 +446,7 @@ for key in "${!aff_pro_arr[@]}"; do
   echo "" 
   echo "Generating the IGV batch file for ${aff_pro_arr[$key]}";
 
-  snap_file=/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${aff_pro_arr[$key]}.snapshot.txt
+  snap_file=/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${aff_pro_arr[$key]}.snapshot.txt
 
   # check if previous version exist, if so - delete it
   if [ -f "${snap_file}" ]; then
@@ -457,7 +457,7 @@ for key in "${!aff_pro_arr[@]}"; do
   # write the header for the IGV batch file
   echo "new" >> ${snap_file}
   echo "genome hg38" >> ${snap_file}
-  echo "snapshotDirectory \"/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}\"" >> ${snap_file}
+  echo "snapshotDirectory \"/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}\"" >> ${snap_file}
   echo "" >> ${snap_file}
 
 
diff --git a/process_NHS_WES_trio.sh b/process_NHS_WES_trio.sh
index bf8b8c0544fb66fcfdf9915e1b3784130594cf11..b31d29bf5e8418281003aa4429a4e3130cc89a7c 100755
--- a/process_NHS_WES_trio.sh
+++ b/process_NHS_WES_trio.sh
@@ -7,12 +7,12 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -24,37 +24,36 @@ DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
 BAMOUT_DIR=${WORK_DIR}/BAMOUT
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 
 # other files to be used
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt							# created by NHS_WES_trio_setup.sh
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt							# created by NHS_WES_trio_setup.sh
-TARGETS=/home/u035/project/resources/DDG2P.20210706.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20210706.clinvar.20210626.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt				# OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt				# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20210706.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20210706.clinvar.20210626.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt			# OK
+TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt			# OK
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk							# points to ../share/gatk4-4.1.8.1-0/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON3=/home/u035/project/software/bcbio/anaconda/bin/python3							# points to python3.6
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-100.4-0/vep
-#REFERENCE_GENOME=/home/u035/project/resources/hg38.fa
-REFERENCE_GENOME=/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
-
-
-
-echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk							# points to ../share/gatk4-4.1.8.1-0/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON3=/home/u035/u035/shared/software/bcbio/anaconda/bin/python3							# points to python3.6
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-100.4-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
+
+
+
+echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/
 echo "BATCH_ID = ${BATCH_ID}"           # the ID of the batch being processed                                   	e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}"           # the PCR plate ID of the batch being currently processed,              	e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"       # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
@@ -158,7 +157,7 @@ mkdir ${G2P_LOG_DIR}
 TXT_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}.report.txt
 HTML_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}.report.html
 #VCF_KEYS='gnomADe|gnomADg'	# old VEP version 97
-VCF_KEYS='gnomADe_GRCh38|gnomADg_r3.0_GRCh38'
+VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
 
 time ${VEP} \
     -i ${IN_FILE} \
@@ -170,11 +169,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 100 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20210706.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.20210706.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 
 echo ""
@@ -248,7 +247,7 @@ cd ${VASE_DIR}
 time ${GATK4} IndexFeatureFile -I ${OUT_FILE}
 
 # select only variants on the 24 chromosomes
-time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${PLATE_ID}_${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/project/resources/24_chr.list --exclude-non-variants
+time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${PLATE_ID}_${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/u035/shared/resources/24_chr.list --exclude-non-variants
 
 # sort the VCF (maybe not needed?, but just in case, and it is quick)
 rm ${PLATE_ID}_${FAMILY_ID}.strict.24chr.sort.denovo.vcf
@@ -505,12 +504,12 @@ done
 
 #################################################################
 # write the IGV batch file for this family based on the bamouts #
-# to be stored as /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.snapshot.txt #
+# to be stored as /scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.snapshot.txt #
 #################################################################
 
 
 
-snap_file=/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.snapshot.txt
+snap_file=/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/bamout_${PROBAND_ID}_${FAMILY_ID}.snapshot.txt
 
 # check if previous version exist, if so - delete it
 if [ -f "${snap_file}" ]; then
@@ -522,7 +521,7 @@ fi
 # write the header for the IGV batch file
 echo "new" >> ${snap_file}
 echo "genome hg38" >> ${snap_file}
-echo "snapshotDirectory \"/scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}\"" >> ${snap_file}
+echo "snapshotDirectory \"/scratch/u035/u035/shared/trio_whole_exome/analysis/${PROJECT_ID}/DECIPHER/IGV/${PLATE_ID}_${FAMILY_ID}\"" >> ${snap_file}
 echo "" >> ${snap_file}
 
 
diff --git a/process_NHS_WES_trio_before_BAMOUT.sh b/process_NHS_WES_trio_before_BAMOUT.sh
index d736a1a120e9b06c4b00fa85efd953df3833e7aa..f6f043ba5b2d1f1007e1b00f29241e967035dad1 100755
--- a/process_NHS_WES_trio_before_BAMOUT.sh
+++ b/process_NHS_WES_trio_before_BAMOUT.sh
@@ -7,12 +7,12 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -23,36 +23,36 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 
 # other files to be used
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt							# created by NHS_WES_trio_setup.sh
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt							# created by NHS_WES_trio_setup.sh
-TARGETS=/home/u035/project/resources/DDG2P.20190919.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt				# OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt				# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt			# OK
+TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt			# OK
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
-REFERENCE_GENOME=/home/u035/project/data/reference/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
+echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/
 echo "BATCH_ID = ${BATCH_ID}"           # the ID of the batch being processed                                   	e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}"           # the PCR plate ID of the batch being currently processed,              	e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"       # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
@@ -153,7 +153,7 @@ G2P_LOG_DIR=${G2P_DIR}/${PLATE_ID}_${FAMILY_ID}_LOG_DIR
 mkdir ${G2P_LOG_DIR}
 TXT_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}.report.txt
 HTML_OUT=${G2P_LOG_DIR}/${PLATE_ID}_${FAMILY_ID}.report.html
-VCF_KEYS='gnomADe|gnomADg'
+VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
 
 
 time ${VEP} \
@@ -166,11 +166,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 97 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.19092019.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-97.3-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.19092019.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.19092019.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-97.3-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.19092019.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 
 echo ""
@@ -226,7 +226,7 @@ cd ${VASE_DIR}
 time ${GATK4} IndexFeatureFile -F ${OUT_FILE}
 
 # select only variants on the 24 chromosomes
-time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${PLATE_ID}_${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/project/resources/24_chr.list --exclude-non-variants
+time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${PLATE_ID}_${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/u035/shared/resources/24_chr.list --exclude-non-variants
 
 # sort the VCF (maybe not needed?, but just in case, and it is quick)
 rm ${PLATE_ID}_${FAMILY_ID}.strict.24chr.sort.denovo.vcf
diff --git a/processing_setup.sh b/processing_setup.sh
index 0356e8dc23b5c80fa3cb63db7e7bfee444707b12..509ce35956eb42f7781c1954c45d48224c855b7a 100755
--- a/processing_setup.sh
+++ b/processing_setup.sh
@@ -7,7 +7,7 @@
 
 
 ### Setup the folder structure for the downstream analysis###
-BASE=/scratch/u035/project/analysis/wes_pilot
+BASE=/scratch/u035/u035/shared/analysis/wes_pilot
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -18,11 +18,11 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 ### Tools
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
 
 
 
diff --git a/run_processing.sh b/run_processing.sh
index f6208eb1756da7bb46d3e447849908699feed610..1e146f0477d9ec97cc29010b12adcb9f4a782dc0 100755
--- a/run_processing.sh
+++ b/run_processing.sh
@@ -7,12 +7,12 @@
  
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 ### folder structure for the downstream analysis - created by processing_setup.sh ###
-BASE=/scratch/u035/project/analysis/wes_pilot
+BASE=/scratch/u035/u035/shared/analysis/wes_pilot
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -23,31 +23,31 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 # other files to be used
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt							# created by processing_setup.sh
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt							# created by processing_setup.sh
-TARGETS=/home/u035/project/resources/DDG2P.20190919.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt                            # OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt                            # OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt                      # OK
+TRANS_MAP=/home/u035/u035/shared/resources/blacklist/current_trans_map.txt                      # OK
 
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
-REFERENCE_GENOME=/home/u035/project/resources/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
@@ -150,7 +150,7 @@ mkdir ${G2P_LOG_DIR}
 TXT_OUT=${G2P_LOG_DIR}/${FAMILY_ID}.report.txt
 HTML_OUT=${G2P_LOG_DIR}/${FAMILY_ID}.report.html
 #VCF_KEYS='gnomADe|gnomADg'	# old VEP
-VCF_KEYS='gnomADe_GRCh38|gnomADg_r3.0_GRCh38'
+VCF_KEYS='gnomADe_r2.1.1_GRCh38|gnomADg_r3.1.1_GRCh38'
 
 
 time ${VEP} \
@@ -163,11 +163,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 100 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.01062020.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.01062020.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.01062020.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.01062020.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 echo ""
 echo ""
@@ -223,7 +223,7 @@ cd ${VASE_DIR}
 time ${GATK4} IndexFeatureFile -F ${OUT_FILE}
 
 # select only variants on the 24 chromosomes
-time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/project/resources/24_chr.list --exclude-non-variants
+time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/u035/shared/resources/24_chr.list --exclude-non-variants
 
 # sort the VCF (maybe not needed?, but just in case, and it is quick)
 rm ${FAMILY_ID}.strict.24chr.sort.denovo.vcf
@@ -237,7 +237,7 @@ time ${GATK4} IndexFeatureFile -F ${FAMILY_ID}.strict.24chr.sort.denovo.vcf
 ########################################################################################################################################
 #### remove variants from LCR and telo-/centro-mere regions
 ###time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${FAMILY_ID}.strict.24chr.sort.denovo.vcf -O ${FAMILY_ID}.clean.denovo.vcf \
-###-XL /home/u035/project/resources/LCR.bed -XL /home/u035/project/resources/sv_repeat_telomere_centromere.bed --exclude-non-variants
+###-XL /home/u035/u035/shared/resources/LCR.bed -XL /home/u035/u035/shared/resources/sv_repeat_telomere_centromere.bed --exclude-non-variants
 
 #### split multi-allelic sites [by -m -any]
 #### left-alignment and normalization [by adding the -f]
diff --git a/submit_depth_of_coverage_MQ20_BQ20.sh b/submit_depth_of_coverage_MQ20_BQ20.sh
index 14e7e34d421f07008e95ddf93c7207075db57f65..0a1a6a64cfdbc0220bec59755a0a71784809236e 100644
--- a/submit_depth_of_coverage_MQ20_BQ20.sh
+++ b/submit_depth_of_coverage_MQ20_BQ20.sh
@@ -18,9 +18,9 @@ then
   fi
 fi
 
-export PATH=$PATH:/home/u035/project/software/bcbio-1.1.3/tools/bin
-BCBIO_CONFIG=/scratch/u035/project/analysis/wes_pilot/bcbio/config
-BCBIO_WORK=/scratch/u035/project/analysis/wes_pilot/bcbio/work
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio-1.1.3/tools/bin
+BCBIO_CONFIG=/scratch/u035/u035/shared/analysis/wes_pilot/bcbio/config
+BCBIO_WORK=/scratch/u035/u035/shared/analysis/wes_pilot/bcbio/work
 
 # Expects environment variables to be set
 # BATCH - date yyyymmdd batch
diff --git a/submit_downstream.sh b/submit_downstream.sh
index ed9006cf54abaa4b03cc6d1758ebf88031030926..ed4ae1c6daed10cfab07d3010d47fb81c093e74a 100755
--- a/submit_downstream.sh
+++ b/submit_downstream.sh
@@ -7,12 +7,12 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 ### folder structure for the downstream analysis - created by downstream_setup.sh###
-BASE=/scratch/u035/project/analysis/wes_pilot
+BASE=/scratch/u035/u035/shared/analysis/wes_pilot
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -23,28 +23,28 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 # other files to be used
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt						# created by downstream_setup.sh
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt						# created by downstream_setup.sh
-TARGETS=/home/u035/project/resources/DDG2P.20190613.plus15bp.merged.bed
-CLINVAR=/home/u035/project/resources/DDG2P.20190613.clinvar.20190603.plus15bp.txt
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20190613.plus15bp.merged.bed
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20190613.clinvar.20190603.plus15bp.txt
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"
-REFERENCE_GENOME=/home/u035/project/data/reference/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
@@ -154,11 +154,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 96 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.13062019.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-96.0-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.13062019.csv',af_from_vcf=1,log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/G2P/genes_in_DDG2P.13062019.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-96.0-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/G2P/DDG2P.13062019.csv',af_from_vcf=1,log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
 
 echo ""
 echo ""
@@ -212,7 +212,7 @@ cd ${VASE_DIR}
 time ${GATK4} IndexFeatureFile -F ${OUT_FILE}
 
 # select only variants on the 24 chromosomes
-time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/project/resources/24_chr.list --exclude-non-variants
+time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${OUT_FILE} -O ${FAMILY_ID}.strict.24chr.denovo.vcf -L /home/u035/u035/shared/resources/24_chr.list --exclude-non-variants
 
 # sort the VCF (maybe not needed?, but just in case, and it is quick)
 rm ${FAMILY_ID}.strict.24chr.sort.denovo.vcf
@@ -224,7 +224,7 @@ time ${GATK4} IndexFeatureFile -F ${FAMILY_ID}.strict.24chr.sort.denovo.vcf
 
 # remove variants from LCR and telo-/centro-mere regions
 time ${GATK4} SelectVariants -R ${REFERENCE_GENOME} -V ${FAMILY_ID}.strict.24chr.sort.denovo.vcf -O ${FAMILY_ID}.clean.denovo.vcf \
--XL /home/u035/project/resources/LCR.bed -XL /home/u035/project/resources/sv_repeat_telomere_centromere.bed --exclude-non-variants
+-XL /home/u035/u035/shared/resources/LCR.bed -XL /home/u035/u035/shared/resources/sv_repeat_telomere_centromere.bed --exclude-non-variants
 
 # split multi-allelic sites [by -m -any]
 # left-alignment and normalization [by adding the -f]
diff --git a/submit_trio_wes_aspera_download.sh b/submit_trio_wes_aspera_download.sh
index 013dcb3e2f1ea2dd2dd5e7c60a902739ddf56e72..c6bb2e99e8f08a638ba8b116f12d941fbc224dcd 100755
--- a/submit_trio_wes_aspera_download.sh
+++ b/submit_trio_wes_aspera_download.sh
@@ -8,16 +8,16 @@
 source $TRANSFER_INFO_FILE
 
 
-/home/u035/project/software/aspera/connect/bin/ascp \
+/home/u035/u035/shared/software/aspera/connect/bin/ascp \
   -T -P 33001 -O 33001 -l 500M -k2 --overwrite=diff \
   $ASPERA_SCP_USER@transfer.genomics.ed.ac.uk:$PROJECT/raw_data \
-  /scratch/u035/project/trio_whole_exome/data
+  /scratch/u035/u035/shared/trio_whole_exome/data
 
 
-cd /scratch/u035/project/trio_whole_exome/data/
+cd /scratch/u035/u035/shared/trio_whole_exome/data/
 mkdir $PROJECT
 mv raw_data $PROJECT/
-cd /scratch/u035/project/trio_whole_exome/data/$PROJECT/raw_data
+cd /scratch/u035/u035/shared/trio_whole_exome/data/$PROJECT/raw_data
 
 
 rm ../md5_check.txt 2> /dev/null
diff --git a/submit_trio_wes_lftp_download.sh b/submit_trio_wes_lftp_download.sh
index f7dba577e6faa2bf01a99e4d10dfdb34a012caec..92e2adaf1a8871be6f10ce75bc258efa7ee02b54 100755
--- a/submit_trio_wes_lftp_download.sh
+++ b/submit_trio_wes_lftp_download.sh
@@ -6,10 +6,10 @@
 #PBS -j oe
 
 ###source $TRANSFER_INFO_FILE
-###/home/u035/project/software/aspera/connect/bin/ascp \
+###/home/u035/u035/shared/software/aspera/connect/bin/ascp \
 ###  -T -P 33001 -O 33001 -l 500M -k2 --overwrite=diff \
 ###  $ASPERA_SCP_USER@transfer.genomics.ed.ac.uk:$PROJECT/raw_data \
-###  /scratch/u035/project/trio_whole_exome/data
+###  /scratch/u035/u035/shared/trio_whole_exome/data
 
 
 PROJ_CONN="login anonymous lftp@ ; mirror -vv ${TOKEN}/${PROJECT}/raw_data  ."
@@ -17,8 +17,8 @@ echo ${PROJ_CONN}
 
 
 # set up an EPCC folder for this project
-mkdir /scratch/u035/project/trio_whole_exome/data/$PROJECT
-cd /scratch/u035/project/trio_whole_exome/data/$PROJECT
+mkdir /scratch/u035/u035/shared/trio_whole_exome/data/$PROJECT
+cd /scratch/u035/u035/shared/trio_whole_exome/data/$PROJECT
 
 
 # download the data
@@ -26,7 +26,7 @@ lftp transfer.genomics.ed.ac.uk <<<${PROJ_CONN}
 
 
 # go into raw_data to perform the md5_check
-# cd /scratch/u035/project/trio_whole_exome/data/$PROJECT/raw_data
+# cd /scratch/u035/u035/shared/trio_whole_exome/data/$PROJECT/raw_data
 
 rm md5_check.txt 2> /dev/null
 for DATE in 20*[0-9]
diff --git a/test_process_NHS_WES_trio.sh b/test_process_NHS_WES_trio.sh
index ab929cfd716fdcf248fcaf09cbbf4007d75b2278..db2c4e04be1dd64da3ee2ae1a97dea4987e71b22 100755
--- a/test_process_NHS_WES_trio.sh
+++ b/test_process_NHS_WES_trio.sh
@@ -7,12 +7,12 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 ### folder structure for the downstream analysis - created by NHS_WES_trio_setup.sh ###
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/trio_whole_exome/analysis
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -23,36 +23,36 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 
 # other files to be used
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt							# created by NHS_WES_trio_setup.sh
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt							# created by NHS_WES_trio_setup.sh
-TARGETS=/home/u035/project/resources/DDG2P.20190919.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
-BLACKLIST=/home/u035/project/resources/current_blacklist.txt				# OK
-TRANS_MAP=/home/u035/project/resources/current_trans_map.txt				# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20190919.clinvar.20190916.plus15bp.txt	# OK
+BLACKLIST=/home/u035/u035/shared/resources/blacklist/current_blacklist.txt			# OK
+TRANS_MAP=/home/u035/u035/shared/resources/trans_map/current_trans_map.txt			# OK
 
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
-REFERENCE_GENOME=/home/u035/project/data/reference/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
 
-echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/project/trio_whole_exome/analysis/output/
+echo "SOURCE_DIR = ${SOURCE_DIR}"       # the general path to the source BAM files (VCF and PED already copied)		i.e. /scratch/u035/u035/shared/trio_whole_exome/analysis/output/
 echo "BATCH_ID = ${BATCH_ID}"           # the ID of the batch being processed                                   	e.g. 11870_Germain_Lorna
 echo "PLATE_ID = ${PLATE_ID}"           # the PCR plate ID of the batch being currently processed,              	e.g. 16862
 echo "PROJECT_ID = ${PROJECT_ID}"       # this the the folder (${BASE}/${PROJECT_ID}) where the downstream analysis will be done
diff --git a/test_run_processing.sh b/test_run_processing.sh
index 81bc65240d1cb1e2bc0ed62cfbafeab9926a4d10..e51fff49d2c6e1bf56f379ac2ac3d99251d61f17 100755
--- a/test_run_processing.sh
+++ b/test_run_processing.sh
@@ -7,12 +7,12 @@
 
 
 # setup PATH
-export PATH=$PATH:/home/u035/project/software/bcbio/anaconda/envs/python2/bin:/home/u035/project/software/bcbio/anaconda/bin
-export PERL5LIB=$PERL5LIB:/home/u035/project/software/bcbio/anaconda/lib/site_perl/5.26.2
+export PATH=$PATH:/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin:/home/u035/u035/shared/software/bcbio/anaconda/bin
+export PERL5LIB=$PERL5LIB:/home/u035/u035/shared/software/bcbio/anaconda/lib/site_perl/5.26.2
 
 
 ### folder structure for the downstream analysis - created by processing_setup.sh ###
-BASE=/scratch/u035/project/analysis/wes_pilot
+BASE=/scratch/u035/u035/shared/analysis/wes_pilot
 WORK_DIR=$BASE/${PROJECT_ID}
 VCF_DIR=${WORK_DIR}/VCF
 PED_DIR=${WORK_DIR}/PED
@@ -23,27 +23,27 @@ COV_DIR=${WORK_DIR}/COV
 DEC_DIR=${WORK_DIR}/DECIPHER
 IGV_DIR=${DEC_DIR}/IGV
 CNV_DIR=${WORK_DIR}/CNV
-SCRIPTS_DIR=/home/u035/project/scripts
+SCRIPTS_DIR=/home/u035/u035/shared/scripts
 
 
 # other files to be used
 FAMILY_IDS=${WORK_DIR}/FAM_IDs.txt							# created by processing_setup.sh
 CHILD_IDS=${WORK_DIR}/PRO_IDs.txt							# created by processing_setup.sh
-TARGETS=/home/u035/project/resources/DDG2P.20190613.plus15bp.merged.bed			# OK
-CLINVAR=/home/u035/project/resources/DDG2P.20190613.clinvar.20190902.plus15bp.txt	# OK
+TARGETS=/home/u035/u035/shared/resources/G2P/DDG2P.20190613.plus15bp.merged.bed			# OK
+CLINVAR=/home/u035/u035/shared/resources/G2P/DDG2P.20190613.clinvar.20190902.plus15bp.txt	# OK
 
 
 ### TOOLS ###
-BCFTOOLS=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bcftools
-BGZIP=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/bgzip
-TABIX=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/tabix
-VT=/home/u035/project/software/bcbio/anaconda/bin/vt
-VASE=/home/u035/project/software/bcbio/anaconda/bin/vase
-GATK4=/home/u035/project/software/bcbio/anaconda/bin/gatk
-GATK3=/home/u035/project/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
-PYTHON2=/home/u035/project/software/bcbio/anaconda/envs/python2/bin/python2.7
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
-REFERENCE_GENOME=/home/u035/project/data/reference/hg38.fa
+BCFTOOLS=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bcftools
+BGZIP=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/bgzip
+TABIX=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/tabix
+VT=/home/u035/u035/shared/software/bcbio/anaconda/bin/vt
+VASE=/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
+GATK4=/home/u035/u035/shared/software/bcbio/anaconda/bin/gatk
+GATK3=/home/u035/u035/shared/software/GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar
+PYTHON2=/home/u035/u035/shared/software/bcbio/anaconda/envs/python2/bin/python2.7
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"	# points to ../share/ensembl-vep-97.3-0/vep
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
 
 
diff --git a/trio_whole_exome_bcbio_crf_template.yaml b/trio_whole_exome_bcbio_crf_template.yaml
index 0d87d96e7ce02e1bcb19e447d83b0b1a31691985..e379642d408852e6aff9309fbc3be6ae0502a6ff 100644
--- a/trio_whole_exome_bcbio_crf_template.yaml
+++ b/trio_whole_exome_bcbio_crf_template.yaml
@@ -19,4 +19,4 @@ details:
   analysis: variant2
   genome_build: hg38
 upload:
-  dir: /scratch/u035/project/trio_whole_exome/analysis/output
+  dir: /scratch/u035/u035/shared/trio_whole_exome/analysis/output
diff --git a/trio_whole_exome_bcbio_template.yaml b/trio_whole_exome_bcbio_template.yaml
index e960be92364ba6eed2dea18cd11361f25b485d69..f6ebbb44f3e55484bf6eab03decdbf5ecb9263f6 100644
--- a/trio_whole_exome_bcbio_template.yaml
+++ b/trio_whole_exome_bcbio_template.yaml
@@ -16,4 +16,4 @@ details:
   analysis: variant2
   genome_build: hg38
 upload:
-  dir: /scratch/u035/project/trio_whole_exome/analysis/output
+  dir: /scratch/u035/u035/shared/trio_whole_exome/analysis/output
diff --git a/trio_whole_exome_config.sh b/trio_whole_exome_config.sh
index e4da287a7b950a0e5bd3636f9fe3ac1488c2cfb5..5c291d3d156d343b7595ed8415980aa939d63033 100644
--- a/trio_whole_exome_config.sh
+++ b/trio_whole_exome_config.sh
@@ -3,13 +3,13 @@
 # Basic configuration options for trio WES pipeline
 #
 
-SCRIPTS=/home/u035/project/scripts
+SCRIPTS=/home/u035/u035/shared/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
+TARGET=/home/u035/u035/shared/resources/exome_targets/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+DOWNLOAD_DIR=/scratch/u035/u035/shared/data
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/analysis
 PARAMS_DIR=$BASE/params
 READS_DIR=$BASE/reads
 CONFIG_DIR=$BASE/config
@@ -18,4 +18,4 @@ OUTPUT_DIR=$BASE/output
 
 ARCHIVE_DIR=/archive/u035/trio_whole_exome
 
-export PATH=/home/u035/project/software/bcbio/tools/bin:$PATH
+export PATH=/home/u035/u035/shared/software/bcbio/tools/bin:$PATH
diff --git a/trio_whole_exome_crf_config.sh b/trio_whole_exome_crf_config.sh
index ce1495088587377cc4007789fad7824eac281f37..3b7a89fdf2e885ce50a550b089645f45c9bcd194 100644
--- a/trio_whole_exome_crf_config.sh
+++ b/trio_whole_exome_crf_config.sh
@@ -3,13 +3,13 @@
 # Basic configuration options for trio WES pipeline
 #
 
-SCRIPTS=/home/u035/project/scripts
+SCRIPTS=/home/u035/u035/shared/scripts
 BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_crf_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
+TARGET=/home/u035/u035/shared/resources/exome_targets/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+DOWNLOAD_DIR=/scratch/u035/u035/shared/data
+REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
-BASE=/scratch/u035/project/trio_whole_exome/analysis
+BASE=/scratch/u035/u035/shared/analysis
 PARAMS_DIR=$BASE/params
 READS_DIR=$BASE/reads
 CONFIG_DIR=$BASE/config
@@ -18,4 +18,4 @@ OUTPUT_DIR=$BASE/output
 
 ARCHIVE_DIR=/archive/u035/trio_whole_exome
 
-export PATH=/home/u035/project/software/bcbio/tools/bin:$PATH
+export PATH=/home/u035/u035/shared/software/bcbio/tools/bin:$PATH
diff --git a/vcf_config.json.backup b/vcf_config.json.backup
index fc5941cb39692ca6ac46a3703cb0d4df1f8f50d6..59464bf2fe878e1df7d9f0d50bab569d787f737f 100644
--- a/vcf_config.json.backup
+++ b/vcf_config.json.backup
@@ -140,7 +140,7 @@
       "species": "homo_sapiens",
       "assembly": "GRCh38",
       "type": "local",
-      "filename_template": "/home/u035/project/resources/gnomad/r3.0/genomes/gnomad.genomes.r3.0.sites.chr###CHR###_trimmed_info.vcf.bgz",
+      "filename_template": "/home/u035/u035/shared/resources/gnomad/r3.0/genomes/gnomad.genomes.r3.0.sites.chr###CHR###_trimmed_info.vcf.bgz",
       "chromosomes": [
         "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
         "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
@@ -201,7 +201,7 @@
       "species": "homo_sapiens",
       "assembly": "GRCh38",
       "type": "local",
-      "filename_template": "/home/u035/project/resources/gnomad/r2.1/exomes/gnomad.exomes.r2.1.sites.grch38.chr###CHR###_noVEP.vcf.gz",
+      "filename_template": "/home/u035/u035/shared/resources/gnomad/r2.1/exomes/gnomad.exomes.r2.1.sites.grch38.chr###CHR###_noVEP.vcf.gz",
       "chromosomes": [
         "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
         "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"