#+ PIPELINE_NAME = GenerateVariomeData.chromosome.v.0.3.0.for.PGI-KPGP-Genome-2012-03.WGS.in.Koref.BiO2.on.2016-07-07 #+ SCRIPT_DIR_PATH = /BiOfs/Live/Jho/Pipeline/GenerateVariomeData.chromosome.v.0.3.0/ #+ WORKSPACE_DIR_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Workspaces/Pipeline.for.WGS/GenerateVariomeData.chromosome.v.0.3.0.on.2016-07-07/ #+ DATA_ID_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Workspaces/Pipeline.for.WGS/GenerateVariomeData.chromosome.v.0.3.0.on.2016-07-07/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 #+ DO_INTEGRATE_PRIOR_GENOTYPE_FILE = None #+ PRIOR_GENOTYPE_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Analyses/VariomeData.to.hg19.with.CleanRead.of.Grade1/VariomeData.0.2/Variome_Data/genotype/{INDIVIDUAL_ID}/variomeData.genotype.allSite.{INDIVIDUAL_ID}.{CHR_NAME}.txt.gz #+ CHR_ALL_SITE_GENOTYPE_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Analyses/GenoType.to.hg19.with.CleanRead.of.Grade1.for.BWA.aln/WGS/{DATA_ID}/{DATA_ID}.{CHR_NAME}.genotype.rs.gz #+ PLOIDY_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Resources/SamplePloidy/{DATA_ID}.ploidy.txt #+ DO_INTEGRATE_PRIOR_SNP_ID = True #+ PRIOR_SNP_ID_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Analyses/VariomeData.to.hg19.with.CleanRead.of.Grade1/VariomeData.0.2/SNP_ID_corrected/snp.id.{CHR_NAME}.txt #+ CHR_ALL_SITE_SNP_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Analyses/SNP.to.hg19.with.CleanRead.of.Grade1.by.MAC.1.MAF.0.00/WGS.of.VariomeData.50.Korean.mapped.by.BWA.aln/SNP/snp.{CHR_NAME}.allSite.txt.gz #+ CHR_VAR_SITE_SNP_ANNOTATION_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Analyses/SNP.to.hg19.with.CleanRead.of.Grade1.by.MAC.1.MAF.0.00/WGS.of.VariomeData.50.Korean.mapped.by.BWA.aln/SNPeff/snp.{CHR_NAME}.varSite.snpEff.vcf #+ CHR_DBSNP_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Resources/Reference/hg19/snp/dbsnp_137.hg19.of.each.chromosome/dbsnp_137.hg19.{CHR_NAME}.vcf #+ CHR_LEN_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Resources/Reference/hg19/chromosome/each/{CHR_NAME}.len.txt #+ DO_SAMPLING = True #+ SAMPLING_OPTION_FILE_PATH = /BiO2/Research/PGI-KPGP-Genome-2012-03/Workspaces/Pipeline.for.WGS/GenerateVariomeData.chromosome.v.0.3.0.on.2016-07-07/inp.sampling/sampling_option.opt #+ SAMPLING_FUNC_LIST = SPLICE-SITE,NON-SYNONYMOUS #+ SAMPLING_MINOR_ALLELE_CHR_COUNT = 3 #+ SAMPLING_MINOR_ALLELE_FREQUENCY = 0.050000 #+ DO_CHECK_CONSISTENCY = True #* chrName : chromosome name. #* pss : position. #* refNt : reference nucleotide. #* snpNts : SNP nucleotides. #* ksId : Korean SNP id. #! chrName pss refNt snpNts ksId chrM 103 G A,G ks12081579 chrM 131 T C,T ks12081580 chrM 143 G A,G ks12081581 chrM 146 T C,T ks12081582 chrM 150 T C,T ks12081583 chrM 151 C C,T ks12081584 chrM 152 T C,T ks12081585 chrM 153 A A,G ks12081586 chrM 189 A A,G ks12081587 chrM 194 C C,T ks12081588 chrM 195 C C,T ks12081589 chrM 197 A A,G ks12081590 chrM 198 C C,T ks12081591 chrM 199 T C,T ks12081592 chrM 200 A A,G ks12081593 chrM 203 G A,G ks12081594 chrM 204 T C,T ks12081595 chrM 214 A A,G ks12681734 chrM 235 A A,G ks12081596 chrM 260 G A,G ks12081597 chrM 311 T C,T ks12081598 chrM 318 G A,G ks12081599 chrM 320 T C,T ks12081600 chrM 328 A A,G ks12081601 chrM 458 C C,T ks12081602 chrM 491 T C,T ks12081603 chrM 548 A A,G ks12081604 chrM 665 A A,G ks12081605 chrM 683 T C,T ks12081606 chrM 711 G A,G ks12081607 chrM 754 C C,T ks12081608 chrM 829 A A,G ks12081609 chrM 963 T C,T ks12081610 chrM 1050 C C,T ks12081611 chrM 1097 T C,T ks12081612 chrM 1109 T C,T ks12081613 chrM 1384 A A,C ks12081614 chrM 1440 G A,G ks12081615 chrM 1600 G A,G ks12081616 chrM 1711 G A,G ks12081617 chrM 1738 A A,G ks12081618 chrM 1945 A A,G ks12081619 chrM 1980 A A,G ks12081620 chrM 2628 T C,T ks12081621 chrM 2708 G A,G ks12081622 chrM 2774 C C,T ks12081623 chrM 2859 T C,T ks12081624 chrM 3012 G A,G ks12081625 chrM 3207 C C,T ks12081626 chrM 3317 G A,G ks12081627 chrM 3369 T C,T ks12081628 chrM 3553 T A,T ks12081629 chrM 3568 C C,T ks12081630 chrM 3730 A A,G ks12081631 chrM 3760 A A,G ks12081632 chrM 3835 G A,G ks12081633 chrM 3961 C C,T ks12681735 chrM 3971 C C,T ks12081634 chrM 4048 T C,T ks12081635 chrM 4049 G A,G ks12081636 chrM 4072 C C,T ks12081637 chrM 4087 C C,T ks12681736 chrM 4114 G A,G ks12081638 chrM 4165 A A,G ks12081639 chrM 4204 A A,G ks12681737 chrM 4249 T C,T ks12081640 chrM 4344 A A,G ks12081641 chrM 4364 T C,T ks12081642 chrM 4387 T C,T ks12081643 chrM 4539 C C,T ks12081644 chrM 4563 A A,G ks12681738 chrM 4656 G A,G ks12081645 chrM 4706 T C,T ks12081646 chrM 4716 A A,G ks12081647 chrM 4733 A A,G ks12081648 chrM 4737 T C,T ks12081649 chrM 4794 A A,G ks12081650 chrM 4825 A A,G ks12081651 chrM 4834 A A,G ks12081652 chrM 4842 G A,G ks12081653 chrM 4884 C C,T ks12081654 chrM 4896 A A,G ks12081655 chrM 4959 A A,G ks12081656 chrM 5050 C C,T ks12081657 chrM 5085 A A,G ks12081658 chrM 5109 T C,T ks12081659 chrM 5148 G A,G ks12081660 chrM 5154 A A,G ks12081661 chrM 5179 C A,C ks12081662 chrM 5191 A A,G ks12081663 chrM 5232 G A,G ks12081664 chrM 5238 G A,G ks12081665 chrM 5264 C C,T ks12081666 chrM 5292 T C,T ks12081667 chrM 5302 A A,G ks12081668 chrM 5352 A A,G ks12081669 chrM 5418 G A,G ks12081670 chrM 5419 T C,T ks12081671 chrM 5461 G A,G ks12081672 chrM 5466 T C,T ks12681739 chrM 5484 T C,T ks12081673 chrM 5540 A A,G ks12081674 chrM 5619 T C,T ks12081675 chrM 5774 G A,G ks12081676 chrM 5807 T C,T ks12081677 chrM 5822 G A,G ks12081678 chrM 5988 C C,T ks12081679 chrM 6027 G A,G ks12081680 chrM 6075 C C,T ks12081681 chrM 6087 T C,T ks12081682 chrM 6126 A A,G ks12681740 chrM 6222 T C,T ks12081683 chrM 6254 T C,T ks12081684 chrM 6268 G A,G ks12081685 chrM 6339 A A,G ks12081686 chrM 6366 T C,T ks12081687 chrM 6393 T C,T ks12081688 chrM 6408 T C,T ks12081689 chrM 6456 C C,T ks12081690 chrM 6504 A A,C ks12081691 chrM 6532 C C,T ks12081692 chrM 6681 T C,T ks12081693 chrM 6748 T C,T ks12081694 chrM 6753 A A,G ks12081695 chrM 6963 G A,G ks12081696 chrM 7197 C A,C ks12081697 chrM 7271 T C,T ks12081698 chrM 7309 A A,T ks12081699 chrM 7373 T C,T ks12081700 chrM 7622 T C,T ks12081701 chrM 7643 G A,G ks12081702 chrM 7650 A A,G ks12681741 chrM 7685 T C,T ks12081703 chrM 7817 C C,T ks12081704 chrM 7854 G A,G ks12081705 chrM 7868 C C,T ks12081706 chrM 7928 C C,T ks12681742 chrM 7959 C A,C ks12081707 chrM 8021 G A,G ks12081708 chrM 8109 A A,G ks12081709 chrM 8201 T C,T ks12081710 chrM 8228 T C,T ks12081711 chrM 8270 G A,G ks12081712 chrM 8309 A A,G ks12081713 chrM 8393 G A,G ks12681743 chrM 8415 C C,T ks12081714 chrM 8474 T C,T ks12081715 chrM 8486 G A,G ks12081716 chrM 8564 A A,G ks12081717 chrM 8585 G A,G ks12081718 chrM 8702 G A,G ks12081719 chrM 8706 T C,T ks12081720 chrM 8765 G A,G ks12081721 chrM 8785 A A,G ks12081722 chrM 8791 G A,G ks12081723 chrM 8794 T C,T ks12081724 chrM 8795 C C,T ks12081725 chrM 8830 C C,T ks12081726 chrM 8857 G A,G ks12081727 chrM 8963 A A,G ks12081728 chrM 8965 C C,T ks12081729 chrM 9011 G A,G ks12081730 chrM 9054 G A,G ks12681744 chrM 9080 A A,G ks12081731 chrM 9091 T C,T ks12081732 chrM 9121 A A,G ks12081733 chrM 9124 G A,G ks12681745 chrM 9181 A A,G ks12081734 chrM 9267 G A,G ks12081735 chrM 9297 C C,T ks12081736 chrM 9302 C C,T ks12081737 chrM 9495 A A,G ks12081738 chrM 9541 C C,T ks12081739 chrM 9546 A A,G ks12081740 chrM 9549 G A,G ks12681746 chrM 9712 C C,T ks12081741 chrM 9825 T A,C,T ks12081742 chrM 9939 T C,T ks12081743 chrM 9951 T C,T ks12081744 chrM 10104 A A,G ks12081745 chrM 10209 T C,T ks12081746 chrM 10239 T C,T ks12681747 chrM 10290 A A,G ks12081747 chrM 10311 G A,G ks12081748 chrM 10346 T C,T ks12081749 chrM 10380 A A,G ks12681748 chrM 10398 A A,G ks12081750 chrM 10399 G A,G ks12081751 chrM 10401 C C,T ks12081752 chrM 10411 T C,T ks12081753 chrM 10610 T C,T ks12081754 chrM 10802 G A,G ks12081755 chrM 10874 C C,T ks12081756 chrM 10883 T C,T ks12081757 chrM 10977 C C,T ks12081758 chrM 10979 A A,G ks12081759 chrM 11018 C C,T ks12081760 chrM 11055 C C,T ks12681749 chrM 11085 A A,G ks12081761 chrM 11216 C C,T ks12081762 chrM 11256 T C,T ks12081763 chrM 11384 T C,T ks12081764 chrM 11537 C C,T ks12081765 chrM 11648 C C,T ks12081766 chrM 11697 G A,G ks12081767 chrM 11888 G A,G ks12081768 chrM 11909 A A,G ks12081769 chrM 11915 G A,G ks12081770 chrM 11945 T C,T ks12081771 chrM 11970 G A,G ks12081772 chrM 12014 A A,G ks12081773 chrM 12027 A A,G ks12081774 chrM 12086 C C,T ks12081775 chrM 12136 C C,T ks12081776 chrM 12359 A A,G ks12081777 chrM 12362 A A,G ks12081778 chrM 12363 C C,T ks12081779 chrM 12373 G A,G ks12081780 chrM 12398 A A,G ks12081781 chrM 12406 C C,T ks12081782 chrM 12407 G A,G ks12081783 chrM 12439 T C,T ks12081784 chrM 12634 C C,T ks12081785 chrM 12673 A A,G ks12081786 chrM 12706 T C,T ks12081787 chrM 12760 C C,T ks12081788 chrM 12772 G A,G ks12081789 chrM 12812 T C,T ks12081790 chrM 12881 T C,T ks12081791 chrM 12883 C C,T ks12081792 chrM 12958 T C,T ks12081793 chrM 13075 A A,G ks12081794 chrM 13105 A A,G ks12081795 chrM 13175 T C,T ks12081796 chrM 13183 T C,T ks12081797 chrM 13234 A A,G ks12081798 chrM 13240 C C,T ks12081799 chrM 13264 A A,G ks12081800 chrM 13438 T C,T ks12081801 chrM 13478 G A,G ks12081802 chrM 13486 A A,G ks12081803 chrM 13652 A A,C,G ks12081804 chrM 13717 A A,G ks12081805 chrM 13760 G A,G ks12681750 chrM 13880 T C,T ks12081806 chrM 13929 G C,G ks12081807 chrM 13943 A A,G ks12081808 chrM 14149 A A,G ks12081809 chrM 14163 G A,G ks12081810 chrM 14179 T C,T ks12081811 chrM 14199 G A,G ks12081812 chrM 14312 T C,T ks12081813 chrM 14319 T C,T ks12081814 chrM 14320 T C,T ks12081815 chrM 14335 C C,T ks12681751 chrM 14341 C C,T ks12081816 chrM 14365 G A,G ks12081817 chrM 14456 C C,T ks12081818 chrM 14477 G A,G ks12081819 chrM 14531 T C,T ks12081820 chrM 14561 G A,G ks12081821 chrM 14570 G A,G ks12081822 chrM 14669 C C,T ks12081823 chrM 14694 A A,G ks12681752 chrM 14774 C C,T ks12681753 chrM 14784 T C,T ks12081824 chrM 14945 C C,T ks12081825 chrM 14979 A A,G ks12081826 chrM 14980 T C,T ks12081827 chrM 15023 C C,T ks12081828 chrM 15044 G A,G ks12081829 chrM 15068 T C,T ks12081830 chrM 15091 T C,T ks12081831 chrM 15140 T C,T ks12081832 chrM 15149 G A,G ks12081833 chrM 15173 G A,G ks12081834 chrM 15185 T C,T ks12081835 chrM 15205 T C,T ks12081836 chrM 15224 C C,T ks12081837 chrM 15251 C C,T ks12081838 chrM 15302 A A,G ks12081839 chrM 15324 G A,G ks12081840 chrM 15460 C C,T ks12081841 chrM 15480 T C,T ks12681754 chrM 15488 A A,T ks12081842 chrM 15498 G A,G ks12081843 chrM 15509 C C,T ks12081844 chrM 15519 C C,T ks12081845 chrM 15536 C C,T ks12081846 chrM 15663 A A,G ks12081847 chrM 15725 A A,G ks12081848 chrM 15735 G A,G ks12081849 chrM 15747 A A,G ks12081850 chrM 15774 G A,G ks12081851 chrM 15785 T C,T ks12081852 chrM 15833 C C,T ks12081853 chrM 15851 T C,T ks12081854 chrM 15852 A A,G ks12081855 chrM 15861 A A,G ks12081856 chrM 15875 A A,G ks12081857 chrM 15884 G A,G ks12081858 chrM 15928 G A,G ks12081859 chrM 15931 G A,G ks12081860 chrM 15955 A A,G ks12081861 chrM 16001 G A,G ks12681755 chrM 16087 T C,T ks12081862 chrM 16094 T C,T ks12081863 chrM 16112 C C,T ks12081864 chrM 16127 T C,T ks12081865 chrM 16130 G A,G ks12081866 chrM 16137 T C,T ks12081867 chrM 16141 T C,T ks12081868 chrM 16146 G A,G ks12081869 chrM 16151 C C,T ks12081870 chrM 16163 A A,G ks12681756 chrM 16165 A A,G ks12081871 chrM 16168 C C,T ks12081872 chrM 16171 A A,G ks12081873 chrM 16172 A A,G ks12081874 chrM 16173 C C,T ks12081875 chrM 16183 A A,C ks12081876 chrM 16185 C A,C ks12081877 chrM 16186 C C,T ks12081878 chrM 16188 C C,T ks12081879 chrM 16189 C C,T ks12081880 chrM 16191 C C,T ks12081881 chrM 16211 T C,T ks12081882 chrM 16219 T C,T ks12081883 chrM 16225 T C,T ks12081884 chrM 16233 T C,T ks12681757 chrM 16234 C A,C ks12081885 chrM 16236 C C,T ks12081886 chrM 16245 T C,T ks12081887 chrM 16250 C C,T ks12081888 chrM 16251 T C,T ks12081889 chrM 16258 C C,T ks12081890 chrM 16259 C A,C ks12081891 chrM 16262 C C,T ks12081892 chrM 16263 C C,T ks12081893 chrM 16267 A A,C ks12081894 chrM 16268 C C,G,T ks12681758 chrM 16268 C C,T ks12081895 chrM 16276 G A,G ks12081896 chrM 16280 C C,T ks12081897 chrM 16292 C C,T ks12081898 chrM 16293 C C,T ks12081899 chrM 16299 T C,T ks12081900 chrM 16300 T C,T ks12081901 chrM 16306 T C,T ks12081902 chrM 16313 T C,T ks12081903 chrM 16321 G A,G ks12081904 chrM 16326 T C,T ks12081905 chrM 16327 T C,T ks12081906 chrM 16329 C C,T ks12081907 chrM 16346 C C,T ks12081908 chrM 16357 C C,T ks12081909 chrM 16359 T C,T ks12081910 chrM 16364 T C,T ks12081911 chrM 16367 C C,T ks12081912 chrM 16401 A A,G ks12681759 chrM 16465 A A,G ks12081913 chrM 16499 A A,G ks12081914 chrM 16521 C C,T ks12081915