From 41e4ff2a4f6eab8b804c3610359c1352eb187f16 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Wed, 21 Jul 2021 11:33:08 +0100
Subject: [PATCH] Updates to prioritization scripts
---
process_NHS_WES_aff_probands.sh | 8 ++++----
process_NHS_WES_quad.sh | 12 ++++++------
process_NHS_WES_trio.sh | 8 ++++----
3 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/process_NHS_WES_aff_probands.sh b/process_NHS_WES_aff_probands.sh
index 5cbd816..3afbfa1 100755
--- a/process_NHS_WES_aff_probands.sh
+++ b/process_NHS_WES_aff_probands.sh
@@ -30,8 +30,8 @@ SCRIPTS_DIR=/home/u035/project/scripts
# other files to be used
-TARGETS=/home/u035/project/resources/DDG2P.20201208.plus15bp.merged.bed # OK
-CLINVAR=/home/u035/project/resources/DDG2P.20201208.clinvar.20201128.plus15bp.txt # OK
+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
@@ -180,9 +180,9 @@ time ${VEP} \
--cache --cache_version 100 \
--dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
--individual all \
- --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20201208.txt" \
+ --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20210706.txt" \
--dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
- --plugin G2P,file='/home/u035/project/resources/DDG2P.20201208.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+ --plugin G2P,file='/home/u035/project/resources/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
echo ""
diff --git a/process_NHS_WES_quad.sh b/process_NHS_WES_quad.sh
index 1a67ebb..87076ef 100755
--- a/process_NHS_WES_quad.sh
+++ b/process_NHS_WES_quad.sh
@@ -30,8 +30,8 @@ SCRIPTS_DIR=/home/u035/project/scripts
# other files to be used
-TARGETS=/home/u035/project/resources/DDG2P.20201208.plus15bp.merged.bed # OK
-CLINVAR=/home/u035/project/resources/DDG2P.20201208.clinvar.20201128.plus15bp.txt # OK
+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
@@ -231,9 +231,9 @@ for KID_ID in ${KID_IDS[@]}; do
--cache --cache_version 100 \
--dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
--individual all \
- --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20201208.txt" \
+ --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20210706.txt" \
--dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
- --plugin G2P,file='/home/u035/project/resources/DDG2P.20201208.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+ --plugin G2P,file='/home/u035/project/resources/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
echo ""
echo ""
@@ -694,9 +694,9 @@ time ${VEP} \
--cache --cache_version 100 \
--dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
--individual all \
- --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.01062020.txt" \
+ --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20210706.txt" \
--dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
- --plugin G2P,file='/home/u035/project/resources/DDG2P.01062020.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+ --plugin G2P,file='/home/u035/project/resources/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
echo ""
diff --git a/process_NHS_WES_trio.sh b/process_NHS_WES_trio.sh
index 38270f6..bf8b8c0 100755
--- a/process_NHS_WES_trio.sh
+++ b/process_NHS_WES_trio.sh
@@ -31,8 +31,8 @@ SCRIPTS_DIR=/home/u035/project/scripts
# other files to be used
FAMILY_IDS=${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.20201208.plus15bp.merged.bed # OK
-CLINVAR=/home/u035/project/resources/DDG2P.20201208.clinvar.20201128.plus15bp.txt # OK
+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
@@ -172,9 +172,9 @@ time ${VEP} \
--cache --cache_version 100 \
--dir_cache /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/vep \
--individual all \
- --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20201208.txt" \
+ --transcript_filter "gene_symbol in /home/u035/project/resources/genes_in_DDG2P.20210706.txt" \
--dir_plugins /home/u035/project/software/bcbio/anaconda/share/ensembl-vep-100.4-0 \
- --plugin G2P,file='/home/u035/project/resources/DDG2P.20201208.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
+ --plugin G2P,file='/home/u035/project/resources/DDG2P.20210706.csv',af_from_vcf=1,confidence_levels='confirmed&probable&both RD and IF',af_from_vcf_keys=${VCF_KEYS},log_dir=${G2P_LOG_DIR},txt_report=${TXT_OUT},html_report=${HTML_OUT}
echo ""
--
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