From 43b11fd09e80327bc3f43ce3b69d1b1cfdd4ece3 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@ed.ac.uk>
Date: Fri, 13 Aug 2021 11:32:06 +0100
Subject: [PATCH] Fix project > u035/shared.
---
docs/Setup_variant_prioritization.md | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/docs/Setup_variant_prioritization.md b/docs/Setup_variant_prioritization.md
index 5323e94..2c282b0 100644
--- a/docs/Setup_variant_prioritization.md
+++ b/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
--
GitLab