diff --git a/process_NHS_WES_aff_probands.sh b/process_NHS_WES_aff_probands.sh index 5cbd8167aa9c6349d95262dd93a45e7b28d1aa97..3afbfa1bedc001209aa6c6944723cf6603d6221e 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 1a67ebb149c0b57c88de7cd99ec122a7ca38e5a5..87076ef01d500e94037f0938b34baad02f5e6d7a 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=${HTML_OUT} echo "" diff --git a/process_NHS_WES_trio.sh b/process_NHS_WES_trio.sh index 38270f6a4220044544a92b2f6eb3516e6447be5e..bf8b8c0544fb66fcfdf9915e1b3784130594cf11 100755 --- a/process_NHS_WES_trio.sh +++ b/process_NHS_WES_trio.sh @@ -31,8 +31,8 @@ SCRIPTS_DIR=/home/u035/project/scripts # other files to be used FAMILY_IDS=${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 ""