Fix project > u035/shared.

docs/Setup_variant_prioritization.md

@@ -21,7 +21,7 @@ Note:			make sure the VEP cache files are tabix converted (significant speedup)
 ### Check the downloaded VEP cache files were tabix converted
 
 ```
-U> ls -l /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep/homo_sapiens_merged/100_GRCh38/<chr>
+U> ls -l /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep/homo_sapiens_merged/100_GRCh38/<chr>
 ```
 
 where <chr> is the chromosome name without the ‘chr’ prefix (e.g., 1,2, ..., 22).
@@ -67,7 +67,7 @@ U> wget ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genot
 U> wget ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad/r2.1/exomes/*.tbi
 ```
 
-Edit the `/home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json` file to update type (remote -> local) and filename_template (local path to datasets) variables for these local datasets.
+Edit the `/home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json` file to update type (remote -> local) and filename_template (local path to datasets) variables for these local datasets.
 
 gnomADg (lines 138-143)
 ```
@@ -76,7 +76,7 @@ gnomADg (lines 138-143)
 "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"
 ```
 
 gnomADe (lines 199-204)
@@ -86,20 +86,20 @@ gnomADe (lines 199-204)
 "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"
 ```
 
 ## Parameter Values for G2P call
 
 Files
-* `/home/u035/project/scripts/process_NHS_WES_trio.sh`
-* `/home/u035/project/scripts/process_NHS_WES_aff_probands.sh` 
+* `/home/u035/u035/shared/scripts/process_NHS_WES_trio.sh`
+* `/home/u035/u035/shared/scripts/process_NHS_WES_aff_probands.sh` 
 
 ```
-VEP="/home/u035/project/software/bcbio/anaconda/bin/perl /home/u035/project/software/bcbio/anaconda/bin/vep"    
+VEP="/home/u035/u035/shared/software/bcbio/anaconda/bin/perl /home/u035/u035/shared/software/bcbio/anaconda/bin/vep"    
 # this points to ../share/ensembl-vep-100.4-0/vep
 
-REFERENCE_GENOME=/home/u035/project/resources/hg38.fa
+REFERENCE_GENOME=/home/u035/u035/shared/resources/hg38.fa
 
 IN_FILE=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}.clean.vcf
 G2P_LOG_DIR=${G2P_DIR}/${PLATE_ID}_${FAMILY_ID}_LOG_DIR
@@ -118,11 +118,11 @@ time ${VEP} \
     --merged \
     --use_given_ref \
     --cache --cache_version 100 \
-    --dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
+    --dir_cache /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/vep \
     --individual all \
-    --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20201208.txt" \
-    --dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
-    --plugin G2P,file='/home/u035/project/resources/DDG2P.20201208.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},\
+    --transcript_filter "gene_symbol in /home/u035/u035/shared/resources/genes_in_DDG2P.20201208.txt" \
+    --dir_plugins /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
+    --plugin G2P,file='/home/u035/u035/shared/resources/DDG2P.20201208.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}
 ```
 
@@ -262,7 +262,7 @@ File name:		clinvar_20210626.P_LP.ACP.vcf
 Description of ClinVar VCF @ `https://www.ncbi.nlm.nih.gov/variation/docs/ClinVar_vcf_files/`
 
 ```
-U> cd /home/u035/project/resources
+U> cd /home/u035/u035/shared/resources
 U> wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20210626.vcf.gz
 U> wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20210626.vcf.gz.tbi
 
@@ -367,7 +367,7 @@ Location at EPCC:	/home/u035/u035/shared/software/bcbio/anaconda/bin/vase
 Parameter Values for VASE STRICT
 
 ```
-VASE=/home/u035/project/software/bin/vase
+VASE=/home/u035/u035/shared/software/bin/vase
 
 IN_FILE=${VCF_DIR}/${PLATE_ID}_${FAMILY_ID}.ready.vcf.gz
 OUT_FILE=${VASE_DIR}/${PLATE_ID}_${FAMILY_ID}.strict.denovo.vcf