修改目录结构

2023-12-15 10:33:49 +08:00 · 2023-12-15 10:33:49 +08:00 · 712d448dd3
parent f31e71b0b7
commit 712d448dd3
65 changed files with 4 additions and 3 deletions
--- a/.gitignore
+++ b/.gitignore
@ -197,5 +197,6 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
-software/
+software
 other
--- a/script/InsertAndDepthStat.R
+++ b/script/InsertAndDepthStat.R
--- a/script/bam_fetch.py
+++ b/script/bam_fetch.py
--- a/script/chemo.py
+++ b/script/chemo.py
--- a/script/correct_genome_3rule.py
+++ b/script/correct_genome_3rule.py
--- a/script/correct_umi_1r_plus_2r.pl
+++ b/script/correct_umi_1r_plus_2r.pl
--- a/script/correct_umi_overlap_reads.py
+++ b/script/correct_umi_overlap_reads.py
--- a/script/correct_umi_subnormal.pl
+++ b/script/correct_umi_subnormal.pl
--- a/script/cromwell.examples.conf
+++ b/script/cromwell.examples.conf
--- a/script/drug_dedup.py
+++ b/script/drug_dedup.py
--- a/script/filter_cnv.pl
+++ b/script/filter_cnv.pl
--- a/script/filter_fusion.pl
+++ b/script/filter_fusion.pl
--- a/script/filter_longindel.pl
+++ b/script/filter_longindel.pl
--- a/script/filter_promoter.pl
+++ b/script/filter_promoter.pl
--- a/script/filter_snpindel.pl
+++ b/script/filter_snpindel.pl
--- a/script/hereditary.py
+++ b/script/hereditary.py
--- a/script/indication.pl
+++ b/script/indication.pl
--- a/script/pollution.py
+++ b/script/pollution.py
--- a/script/postprocess.py
+++ b/script/postprocess.py
--- a/script/public/bed/160.bed
+++ b/script/public/bed/160.bed
--- a/script/public/bed/17.bed
+++ b/script/public/bed/17.bed
--- a/script/public/bed/624.bed
+++ b/script/public/bed/624.bed
--- a/script/public/bed/650.bed
+++ b/script/public/bed/650.bed
--- a/script/public/bed/lung17gene.hg19.liftover.bed
+++ b/script/public/bed/lung17gene.hg19.liftover.bed
--- a/script/public/blacklist.txt
+++ b/script/public/blacklist.txt
--- a/script/public/chemo_database.xlsx
+++ b/script/public/chemo_database.xlsx
--- a/script/public/cnvkit/160gene_pool_normal_reference.cnn
+++ b/script/public/cnvkit/160gene_pool_normal_reference.cnn
--- a/script/public/cnvkit/17gene_pool_normal_reference.cnn
+++ b/script/public/cnvkit/17gene_pool_normal_reference.cnn
--- a/script/public/cnvkit/access-5k-mappable.hg19.bed
+++ b/script/public/cnvkit/access-5k-mappable.hg19.bed
--- a/script/public/cnvkit/refFlat.txt
+++ b/script/public/cnvkit/refFlat.txt
--- a/script/public/gene_strand.txt
+++ b/script/public/gene_strand.txt
--- a/script/public/hereditary_database.xlsx
+++ b/script/public/hereditary_database.xlsx
--- a/script/public/hg19_refGene.txt
+++ b/script/public/hg19_refGene.txt
--- a/script/public/hotspot/hotspot-info.xlsx
+++ b/script/public/hotspot/hotspot-info.xlsx
--- a/script/public/hotspot/hotspot.py
+++ b/script/public/hotspot/hotspot.py
--- a/script/public/hotspot/hotspot_delins.bed
+++ b/script/public/hotspot/hotspot_delins.bed
--- a/script/public/hotspot/hotspot_snv.txt
+++ b/script/public/hotspot/hotspot_snv.txt
--- a/script/public/hotspot/hotspot_snv.vcf
+++ b/script/public/hotspot/hotspot_snv.vcf
--- a/script/public/noise/160.cfdna.back.txt
+++ b/script/public/noise/160.cfdna.back.txt
--- a/script/public/noise/160.tissue.back.txt
+++ b/script/public/noise/160.tissue.back.txt
--- a/script/public/noise/17.cfdna.back.txt
+++ b/script/public/noise/17.cfdna.back.txt
--- a/script/public/noise/17.tissue.back.txt
+++ b/script/public/noise/17.tissue.back.txt
--- a/script/public/noise/624.cfdna.back.txt
+++ b/script/public/noise/624.cfdna.back.txt
--- a/script/public/noise/682.tissue.back.txt
+++ b/script/public/noise/682.tissue.back.txt
--- a/script/public/pollution/160_contaminate_ref.bed
+++ b/script/public/pollution/160_contaminate_ref.bed
--- a/script/public/pollution/17_contaminate_ref.bed
+++ b/script/public/pollution/17_contaminate_ref.bed
--- a/script/public/pollution/624_contaminate_cnvkit.bed
+++ b/script/public/pollution/624_contaminate_cnvkit.bed
--- a/script/public/pollution/624_contaminate_ref.bed
+++ b/script/public/pollution/624_contaminate_ref.bed
--- a/script/public/pollution/682_contaminate_cnvkit.bed
+++ b/script/public/pollution/682_contaminate_cnvkit.bed
--- a/script/public/pollution/682_contaminate_ref.bed
+++ b/script/public/pollution/682_contaminate_ref.bed
--- a/script/public/pollution/contaminate_650.bed
+++ b/script/public/pollution/contaminate_650.bed
--- a/script/qc_stat.py
+++ b/script/qc_stat.py
--- a/script/run_pipeline.py
+++ b/script/run_pipeline.py
--- a/script/run_wdl.py
+++ b/script/run_wdl.py
--- a/script/sample_post.py
+++ b/script/sample_post.py
--- a/script/soft_bash
+++ b/script/soft_bash
--- a/script/target_therapy_cnv.pl
+++ b/script/target_therapy_cnv.pl
--- a/script/target_therapy_fusion.pl
+++ b/script/target_therapy_fusion.pl
--- a/script/target_therapy_longindel.pl
+++ b/script/target_therapy_longindel.pl
--- a/script/target_therapy_snpindel.pl
+++ b/script/target_therapy_snpindel.pl
--- a/script/vcf_add_tag_msi.pl
+++ b/script/vcf_add_tag_msi.pl
--- a/script/vcf_add_tag_mutalt.py
+++ b/script/vcf_add_tag_mutalt.py
--- a/script/vcf_filter.py
+++ b/script/vcf_filter.py
--- a/script/vcf_operations.py
+++ b/script/vcf_operations.py
--- a/database/info.csv
+++ b/database/info.csv
@ -19,8 +19,8 @@ LZ168,Ovarian_87_gene,卵巢癌87基因检测（组织版）,卵巢癌87基因
 LZ169,Ovarian_87_gene,卵巢癌87基因检测（血液版）,卵巢癌87基因检测报告（血液版）,addTarget;addFusion;addCnv;addMmr;addChemo;addHcs,ST01,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/CCND1/HRAS/MAP2K1/ARID1A/CTNNB1/ERBB4/MDM2/MSH2/MSH6/PMS2/EPCAM,MET,NA,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1/MDM2/CCND1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3/CYP19A1/CYP2D6,BRCA1/BRCA2/EPCAM/MLH1/MSH2/MSH6/PMS2,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
 LZ170,Cervical_84_gene,宫颈癌84基因检测（组织版）,宫颈癌84基因检测报告（组织版）,addTarget;addFusion;addCnv;addMsi;addMmr;addChemo,ST12,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/FBXW7/ARID1A/STK11/NOTCH1/MSH2/MSH6/PMS2/EPCAM,MET,NA,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3/CYP19A1/CYP2D6,NA,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
 LZ171,Cervical_84_gene,宫颈癌84基因检测（血液版）,宫颈癌84基因检测报告（血液版）,addTarget;addFusion;addCnv;addMmr;addChemo,ST12,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/FBXW7/ARID1A/STK11/NOTCH1/MSH2/MSH6/PMS2/EPCAM,MET,NA,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3/CYP19A1/CYP2D6,NA,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
-LZ172,Uterine_84_gene,子宫内膜癌84基因检测（组织版）,子宫内膜癌84基因检测报告（组织版）,addTarget;addFusion;addCnv;addMsi;addMmr;addChemo;addHcs,ST23,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/CTNNB1/ARID1A/POLE/FBXW7/MSH2/MSH6/PMS2/EPCAM,MET,NA,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3/CYP19A1/CYP2D6,EPCAM/MLH1/MSH2/MSH6/PMS2,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
+LZ172,Uterine_84_gene,子宫内膜癌84基因检测（组织版）,子宫内膜癌84基因检测报告（组织版）,addTarget;addFusion;addCnv;addMsi;addMmr;addChemo;addHcs;addMtec,ST23,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/CTNNB1/ARID1A/POLE/FBXW7/MSH2/MSH6/PMS2/EPCAM,MET,NA,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3/CYP19A1/CYP2D6,EPCAM/MLH1/MSH2/MSH6/PMS2,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
-LZ173,Uterine_84_gene,子宫内膜癌84基因检测（血液版）,子宫内膜癌84基因检测报告（血液版）,addTarget;addFusion;addCnv;addMmr;addChemo;addHcs,ST23,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/CTNNB1/ARID1A/POLE/FBXW7/MSH2/MSH6/PMS2/EPCAM,MET,NA,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3/CYP19A1/CYP2D6,EPCAM/MLH1/MSH2/MSH6/PMS2,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
+LZ173,Uterine_84_gene,子宫内膜癌84基因检测（血液版）,子宫内膜癌84基因检测报告（血液版）,addTarget;addFusion;addCnv;addMmr;addChemo;addHcs;addMtec,ST23,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/CTNNB1/ARID1A/POLE/FBXW7/MSH2/MSH6/PMS2/EPCAM,MET,NA,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3/CYP19A1/CYP2D6,EPCAM/MLH1/MSH2/MSH6/PMS2,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
 LZ174,Liver_83_gene,肝癌83基因检测（组织版）,肝癌83基因检测报告（组织版）,addTarget;addFusion;addCnv;addMsi;addMmr;addChemo,ST26,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/CTNNB1/ERBB4/TERT/ARID1A/JAK1/MSH2/MSH6/PMS2/EPCAM,MET,TERT,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3,NA,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
 LZ175,Liver_83_gene,肝癌83基因检测（血液版）,肝癌83基因检测报告（血液版）,addTarget;addFusion;addCnv;addMmr;addChemo,ST26,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/CTNNB1/ERBB4/TERT/ARID1A/JAK1/MSH2/MSH6/PMS2/EPCAM,MET,TERT,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3,NA,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA
 LZ176,Biliary_84_gene,胆系肿瘤84基因检测（组织版）,胆道癌84基因检测报告（组织版）,addTarget;addFusion;addCnv;addMsi;addMmr;addChemo,ST06,160,AKT1/ALK/ATM/ATR/BARD1/BRAF/BRCA1/BRCA2/BRIP1/CCND2/CCND3/CDK12/CDK4/CDKN2A/CHEK1/CHEK2/CSF1R/EGFR/ERBB2/FANCA/FANCL/FGFR1/FGFR2/FGFR3/IDH1/KIT/KRAS/MET/MLH1/MTOR/NBN/NF1/NRAS/NTRK1/NTRK2/NTRK3/PALB2/PDGFRA/PIK3CA/PTEN/RAD51B/RAD51C/RAD51D/RAD54L/RB1/RET/ROS1/SDHA/SDHB/SDHC/SDHD/SMO/TP53/TSC1/TSC2/MDM2/ARID1A/SMAD4/CTNNB1/APC/FBXW7/MSH2/MSH6/PMS2/EPCAM,MET,NA,ALK/CCND2/CCND3/CDK4/CDKN2A/CSF1R/EGFR/ERBB2/FGFR1/FGFR2/FGFR3/MET/RB1/MDM2,ALK/NTRK1/NTRK2/NTRK3/RET/ROS1,NA,ABCB1/CASP7/CDA/CYP2C8/CYP3A4/DPYD/DYNC2H1/ERCC1/ERCC2/GSTP1/MTHFR/NQO1/SOD2/TPMT/TYMS/UGT1A1/XRCC1/XPC/HAS3,NA,MSH2/MSH6/MLH1/PMS2/EPCAM,NA,NA,NA