#+ PIPELINE_NAME = Generate_Variome_Data.chromosome.v.0.3.10.for.KRISS-Korean-Variome-2012-03.in.KOGIC.Lion.on.2019-11-28 #+ SCRIPT_DIR_PATH = /BiO/Share/Live/Jho/Pipeline/Generate_Variome_Data.chromosome.v.0.3.10/ #+ WORKSPACE_DIR_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Workspace/Pipeline.by.Sungwoong.Jho/Generate_Variome_Data.chromosome.v.0.3.10.on.2019-11-28/ #+ DATA_ID_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Workspace/Pipeline.by.Sungwoong.Jho/Generate_Variome_Data.chromosome.v.0.3.10.on.2019-11-28/inp_data_id/data_id_list.txt #+ CHR_NAME_LIST = chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM #+ CHR_DBSNP_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Resource/Reference/hg19/snp/GATK-bundle-2.5/dbsnp_137.hg19.of.each.chromosome/dbsnp_137.hg19.{CHR_NAME}.vcf #+ CHR_SEQ_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Resource/Reference/hg19/chromosome/each/{CHR_NAME}.upper.fa #+ CHR_LEN_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Resource/Reference/hg19/chromosome/each/{CHR_NAME}.len.txt #+ CMD_BCFTOOLS = /BiO/Share/Live/Jho/Program/bcftools-1.3.1/bcftools #+ PROCESSING_BLOCK_SIZE = 30000000 #+ UNCERTAINTY_PLATFORM_DATA_COUNT_MIN = 5 #+ CHR_ALL_SITE_GENOTYPE_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/GenoType.to.hg19.by.GATK.UnifiedGenotyper/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/{DATA_ID}/{DATA_ID}.{CHR_NAME}.genotype.rs.gz #+ PLOIDY_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Resource/Sample_Ploidy/{DATA_ID}.ploidy.txt #+ DO_INTEGRATE_PRIOR_GENOTYPE_FILE = True #+ PRIOR_GENOTYPE_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/VariomeData.to.hg19/VariomeData.0.7/Supplementary_Data/genotype/{INDIVIDUAL_ID}/variomeData.genotype.allSite.{INDIVIDUAL_ID}.{CHR_NAME}.txt.gz #+ SNP_ID_PREFIX = ks #+ DO_INTEGRATE_PRIOR_SNP_ID = True #+ PRIOR_SNP_ID_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/VariomeData.to.hg19/VariomeData.0.7/ID/snp_id/snp.id.{CHR_NAME}.txt #+ CHR_ALL_SITE_SNP_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/SNP.to.hg19.by.MAC.1.MAF.0.00.from.GenoType/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/VariomeData.200.Korean.with.Extended.Statistics/SNP/snp.{CHR_NAME}.allSite.txt.gz #+ CHR_VAR_SITE_SNP_ANNOTATION_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/SNP.to.hg19.by.MAC.1.MAF.0.00.from.GenoType/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/VariomeData.200.Korean.with.Extended.Statistics/SNPeff/snp.{CHR_NAME}.varSite.snpEff.vcf #+ INDEL_ID_PREFIX = ki #+ DO_INTEGRATE_PRIOR_INDEL_ID = True #+ PRIOR_INDEL_ID_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/VariomeData.to.hg19/VariomeData.0.7/ID/indel_id/indel.id.{CHR_NAME}.txt #+ INDEL_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/IDP.to.hg19.by.FreeBayes/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/VariomeData.200.Korean/IDP/IDP.vcf #+ CNV_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/CNV.to.hg19.by.CNVnator/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/{DATA_ID}/{DATA_ID}.cnvnator.cnv #+ DO_INTEGRATE_PRIOR_CNV_FILE = True #+ PRIOR_CNV_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/VariomeData.to.hg19/VariomeData.0.7/Supplementary_Data/cnv/{INDIVIDUAL_ID}.cnv.cnvnator.tsv #+ BD_SV_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/SV.to.hg19.by.BreakDancer/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/{DATA_ID}/{DATA_ID}.breakdancer.sv #+ DO_INTEGRATE_PRIOR_BD_SV_FILE = False #+ PRIOR_BD_SV_FILE_PATH = None #+ DE_SV_TYPE_LIST = BND,DEL,DUP,INS,INV #+ DE_SV_BCF_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/SV.to.hg19.by.DELLY/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/{DATA_ID}/{DATA_ID}.delly.{SV_TYPE}.bcf #+ DO_INTEGRATE_PRIOR_DE_SV_FILE = True #+ PRIOR_DE_SV_BCF_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/VariomeData.to.hg19/VariomeData.0.7/Supplementary_Data/sv/{INDIVIDUAL_ID}/{INDIVIDUAL_ID}.sv.delly.{SV_TYPE}.bcf #+ PRIOR_DE_SV_CSI_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/VariomeData.to.hg19/VariomeData.0.7/Supplementary_Data/sv/{INDIVIDUAL_ID}/{INDIVIDUAL_ID}.sv.delly.{SV_TYPE}.bcf.csi #+ DO_INTEGRATE_PRIOR_SAMPLE_INFORMATION = True #+ PRIOR_SAMPLE_INFORMATION_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/VariomeData.to.hg19/VariomeData.0.7/Supplementary_Data/sample_information/sample_information.tsv #+ EXT_CHR_ALL_SITE_SNP_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/SNP.to.hg19.by.MAC.1.MAF.0.00.from.GenoType/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/VariomeData.200.Core.100.Rest.Korean.with.Extended.Statistics/SNP/snp.{CHR_NAME}.allSite.txt.gz #+ EXT_CHR_VAR_SITE_SNP_ANNOTATION_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/SNP.to.hg19.by.MAC.1.MAF.0.00.from.GenoType/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/VariomeData.200.Core.100.Rest.Korean.with.Extended.Statistics/SNPeff/snp.{CHR_NAME}.varSite.snpEff.vcf #+ EXT_INDEL_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Analysis/IDP.to.hg19.by.FreeBayes/WGS.of.CleanRead.of.Grade1.mapped.by.BWA.aln/VariomeData.200.Core.100.Rest.Korean/IDP/IDP.vcf #+ DO_CHECK_CONSISTENCY = True #+ DO_SAMPLING = True #+ SAMPLING_OPTION_FILE_PATH = /BiO/Research/Project1/KRISS-Korean-Variome-2012-03/Variome_Data_Generation/Workspace/Pipeline.by.Sungwoong.Jho/Generate_Variome_Data.chromosome.v.0.3.10.on.2019-11-28/inp_sampling/sampling_option.opt #+ SAMPLING_SNP_FUNC_LIST = SPLICE-SITE,NON-SYNONYMOUS #+ SAMPLING_SNP_MINOR_ALLELE_CHR_COUNT = 3 #+ SAMPLING_SNP_MINOR_ALLELE_FREQUENCY = 0.050000 #+ SAMPLING_INDEL_FUNC_LIST = SPLICE-SITE,CODON_CHANGE,FRAME_SHIFT #+ SAMPLING_INDEL_MINOR_ALLELE_CHR_COUNT = 3 #+ SAMPLING_INDEL_MINOR_ALLELE_FREQUENCY = 0.050000 #+ SAMPLING_DE_SV_INS_SIZE_MAX = 23 #* chrName : Chromosome name. #* pss : position. #* refSeq : Reference sequence. #* indelSeqs : INDEL sequences. #* indelId : INDEL id. #! chrName pss refSeq indelSeqs indelId chrM 42 T T,TC ki1960468 chrM 151 CT C,CT ki1960469 chrM 152 T T,TC ki1960470 chrM 247 GA G,GA ki1960471 chrM 302 ACCC A,AC,ACC,ACCC,ACCCC ki1960472 chrM 302 ACCC A,ACC,ACCC ki2334101 chrM 453 A A,AT ki1960473 chrM 457 T T,TC ki3142671 chrM 514 AGC A,AGC ki3142672 chrM 515 G G,GCA ki3142673 chrM 515 GCA G,GCA ki2334102 chrM 515 GCA G,GCA,GCACA ki1960474 chrM 569 A A,AC ki3142674 chrM 569 A A,AC,ACC ki1960475 chrM 569 A A,ACC ki2334103 chrM 595 T T,TC ki3142675 chrM 957 A A,AC ki2334104 chrM 957 AC A,AC,ACC ki1960476 chrM 2152 T T,TA ki1960477 chrM 2228 T T,TA ki1960478 chrM 3168 T T,TC ki3594721 chrM 5895 A A,AC,ACC ki1960479 chrM 5898 C C,CT ki3142676 chrM 8265 CT C,CT ki3594722 chrM 8271 CACCCCCTCT C,CACCCCCTCT ki3594723 chrM 15940 CT C,CT ki3594724 chrM 16179 TC T,TC ki3142677 chrM 16180 C C,CA ki3142678 chrM 16180 C C,CA,CG ki3594725 chrM 16183 ACC A,AACCC,ACC ki3142679 chrM 16183 ACC A,ACC ki1960480