#+ PIPELINE_NAME = variomeDataGeneration.chromosome.v.0.0.0.for.PGI-KPGP-Genome-2012-03.on.2014-06-16.in.Tiger #+ SCRIPT_DIR_PATH = /BiOfs/BioPeople/swjho/pipeline/variomeDataGeneration.chromosome.v.0.0.0/script/ #+ WORKSPACE_DIR_PATH = /BiO/BioPeople/swjho/analyze/PGI-KPGP-Genome-2012-03/VariomeData.to.hg19.with.CleanRead.of.Grade1/WGS/using.pipeline.variomeDataGeneration.chromosome.v.0.0.0.on.2014-06-16/ #+ DATA_NAME_LIST = KPGP-00001,KPGP-00002,KPGP-00006,KPGP-00032,KPGP-00033,KPGP-00088,KPGP-00090,KPGP-00117,KPGP-00120,KPGP-00121,KPGP-00122,KPGP-00124,KPGP-00125,KPGP-00127,KPGP-00128,KPGP-00129,KPGP-00131,KPGP-00132,KPGP-00134,KPGP-00136,KPGP-00137,KPGP-00138,KPGP-00139,KPGP-00141,KPGP-00142,KPGP-00144,KPGP-00145,KPGP-00220,KPGP-00224,KPGP-00227,KPGP-00228,KPGP-00229,KPGP-00230,KPGP-00232,KPGP-00233,KPGP-00235,KPGP-00254 #+ 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_GENERATE_VARIOME_DATA_FROM_GENOTYPE = True #+ CHR_ALL_SITE_GENOTYPE_FILE_PATH = /BiO/BioProjects/PGI-KPGP-Genome-2012-03/Analyses/GenoType.to.hg19.with.CleanRead.of.Grade1/WGS/{DATA_NAME}/{DATA_NAME}.{CHR_NAME}.genotype.rs.gz #+ PLOIDY_FILE_PATH = /BiO/BioProjects/PGI-KPGP-Genome-2012-03/Resources/Sample_Ploidy/{DATA_NAME}.ploidy.txt #+ DO_GENERATE_VARIOME_DATA_FROM_SNP = True #+ CHR_ALL_SITE_SNP_FILE_PATH = /BiO/BioProjects/PGI-KPGP-Genome-2012-03/Analyses/SNP.to.hg19.with.CleanRead.of.Grade1/WGS/SNP/snp.{CHR_NAME}.allSite.txt.gz #+ CHR_VAR_SITE_SNP_ANNOTATION_FILE_PATH = /BiO/BioProjects/PGI-KPGP-Genome-2012-03/Analyses/SNP.to.hg19.with.CleanRead.of.Grade1/WGS/SNPeff/snp.{CHR_NAME}.varSite.snpEff.vcf #+ CHR_DBSNP_FILE_PATH = /BiO/BioProjects/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 = /BiO/BioProjects/PGI-KPGP-Genome-2012-03/Resources/Reference/hg19/chromosome/each/{CHR_NAME}.len.txt #* 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 ks11242861 chrM 131 T C,T ks11242862 chrM 143 G A,G ks11242863 chrM 146 T C,T ks11242864 chrM 150 T C,T ks11242865 chrM 151 C C,T ks11242866 chrM 152 T C,T ks11242867 chrM 153 A A,G ks11242868 chrM 189 A A,G ks11242869 chrM 194 C C,T ks11242870 chrM 195 C C,T ks11242871 chrM 197 A A,G ks11242872 chrM 198 C C,T ks11242873 chrM 199 T C,T ks11242874 chrM 200 A A,G ks11242875 chrM 203 G A,G ks11242876 chrM 204 T C,T ks11242877 chrM 235 A A,G ks11242878 chrM 260 G A,G ks11242879 chrM 311 T C,T ks11242880 chrM 318 G A,G ks11242881 chrM 320 T C,T ks11242882 chrM 328 A A,G ks11242883 chrM 458 C C,T ks11242884 chrM 491 T C,T ks11242885 chrM 548 A A,G ks11242886 chrM 665 A A,G ks11242887 chrM 683 T C,T ks11242888 chrM 711 G A,G ks11242889 chrM 754 C C,T ks11242890 chrM 829 A A,G ks11242891 chrM 963 T C,T ks11242892 chrM 1050 C C,T ks11242893 chrM 1097 T C,T ks11242894 chrM 1109 T C,T ks11242895 chrM 1384 A A,C ks11242896 chrM 1440 G A,G ks11242897 chrM 1600 G A,G ks11242898 chrM 1711 G A,G ks11242899 chrM 1738 A A,G ks11242900 chrM 1980 A A,G ks11242901 chrM 2628 T C,T ks11242902 chrM 2708 G A,G ks11242903 chrM 2774 C C,T ks11242904 chrM 2859 T C,T ks11242905 chrM 3012 G A,G ks11242906 chrM 3207 C C,T ks11242907 chrM 3317 G A,G ks11242908 chrM 3369 T C,T ks11242909 chrM 3553 T A,T ks11242910 chrM 3568 C C,T ks11242911 chrM 3760 A A,G ks11242912 chrM 3835 G A,G ks11242913 chrM 3971 C C,T ks11242914 chrM 4048 T C,T ks11242915 chrM 4049 G A,G ks11242916 chrM 4072 C C,T ks11242917 chrM 4114 G A,G ks11242918 chrM 4165 A A,G ks11242919 chrM 4249 T C,T ks11242920 chrM 4344 A A,G ks11242921 chrM 4387 T C,T ks11242922 chrM 4539 C C,T ks11242923 chrM 4656 G A,G ks11242924 chrM 4706 T C,T ks11242925 chrM 4716 A A,G ks11242926 chrM 4733 A A,G ks11242927 chrM 4737 T C,T ks11242928 chrM 4794 A A,G ks11242929 chrM 4825 A A,G ks11242930 chrM 4834 A A,G ks11242931 chrM 4842 G A,G ks11242932 chrM 4884 C C,T ks11242933 chrM 4896 A A,G ks11242934 chrM 4959 A A,G ks11242935 chrM 5050 C C,T ks11242936 chrM 5085 A A,G ks11242937 chrM 5109 T C,T ks11242938 chrM 5148 G A,G ks11242939 chrM 5154 A A,G ks11242940 chrM 5179 C A,C ks11242941 chrM 5191 A A,G ks11242942 chrM 5232 G A,G ks11242943 chrM 5238 G A,G ks11242944 chrM 5292 T C,T ks11242945 chrM 5302 A A,G ks11242946 chrM 5352 A A,G ks11242947 chrM 5418 G A,G ks11242948 chrM 5419 T C,T ks11242949 chrM 5461 G A,G ks11242950 chrM 5484 T C,T ks11242951 chrM 5619 T C,T ks11242952 chrM 5774 G A,G ks11242953 chrM 5807 T C,T ks11242954 chrM 5822 G A,G ks11242955 chrM 5988 C C,T ks11242956 chrM 6075 C C,T ks11242957 chrM 6087 T C,T ks11242958 chrM 6222 T C,T ks11242959 chrM 6254 T C,T ks11242960 chrM 6268 G A,G ks11242961 chrM 6339 A A,G ks11242962 chrM 6366 T C,T ks11242963 chrM 6393 T C,T ks11242964 chrM 6408 T C,T ks11242965 chrM 6456 C C,T ks11242966 chrM 6532 C C,T ks11242967 chrM 6681 T C,T ks11242968 chrM 6748 T C,T ks11242969 chrM 6963 G A,G ks11242970 chrM 7197 C A,C ks11242971 chrM 7271 T C,T ks11242972 chrM 7309 A A,T ks11242973 chrM 7622 T C,T ks11242974 chrM 7643 G A,G ks11242975 chrM 7685 T C,T ks11242976 chrM 7817 C C,T ks11242977 chrM 7854 G A,G ks11242978 chrM 7868 C C,T ks11242979 chrM 7959 C A,C ks11242980 chrM 8021 G A,G ks11242981 chrM 8109 A A,G ks11242982 chrM 8201 T C,T ks11242983 chrM 8270 G A,G ks11242984 chrM 8309 A A,G ks11242985 chrM 8415 C C,T ks11242986 chrM 8474 T C,T ks11242987 chrM 8564 A A,G ks11242988 chrM 8585 G A,G ks11242989 chrM 8702 G A,G ks11242990 chrM 8706 T C,T ks11242991 chrM 8765 G A,G ks11242992 chrM 8785 A A,G ks11242993 chrM 8791 G A,G ks11242994 chrM 8795 C C,T ks11242995 chrM 8830 C C,T ks11242996 chrM 8857 G A,G ks11242997 chrM 8963 A A,G ks11242998 chrM 8965 C C,T ks11242999 chrM 9011 G A,G ks11243000 chrM 9080 A A,G ks11243001 chrM 9121 A A,G ks11243002 chrM 9181 A A,G ks11243003 chrM 9267 G A,G ks11243004 chrM 9297 C C,T ks11243005 chrM 9495 A A,G ks11243006 chrM 9541 C C,T ks11243007 chrM 9546 A A,G ks11243008 chrM 9712 C C,T ks11243009 chrM 9825 T A,C,T ks11243010 chrM 9951 T C,T ks11243011 chrM 10104 A A,G ks11243012 chrM 10290 A A,G ks11243013 chrM 10311 G A,G ks11243014 chrM 10346 T C,T ks11243015 chrM 10398 A A,G ks11243016 chrM 10399 G A,G ks11243017 chrM 10401 C C,T ks11243018 chrM 10411 T C,T ks11243019 chrM 10610 T C,T ks11243020 chrM 10802 G A,G ks11243021 chrM 10874 C C,T ks11243022 chrM 10883 T C,T ks11243023 chrM 10977 C C,T ks11243024 chrM 10979 A A,G ks11243025 chrM 11018 C C,T ks11243026 chrM 11085 A A,G ks11243027 chrM 11216 C C,T ks11243028 chrM 11256 T C,T ks11243029 chrM 11384 T C,T ks11243030 chrM 11537 C C,T ks11243031 chrM 11648 C C,T ks11243032 chrM 11697 G A,G ks11243033 chrM 11888 G A,G ks11243034 chrM 11915 G A,G ks11243035 chrM 11945 T C,T ks11243036 chrM 11970 G A,G ks11243037 chrM 12014 A A,G ks11243038 chrM 12027 A A,G ks11243039 chrM 12136 C C,T ks11243040 chrM 12359 A A,G ks11243041 chrM 12362 A A,G ks11243042 chrM 12373 G A,G ks11243043 chrM 12398 A A,G ks11243044 chrM 12406 C C,T ks11243045 chrM 12407 G A,G ks11243046 chrM 12439 T C,T ks11243047 chrM 12634 C C,T ks11243048 chrM 12706 T C,T ks11243049 chrM 12760 C C,T ks11243050 chrM 12772 G A,G ks11243051 chrM 12812 T C,T ks11243052 chrM 12881 T C,T ks11243053 chrM 12883 C C,T ks11243054 chrM 12958 T C,T ks11243055 chrM 13075 A A,G ks11243056 chrM 13105 A A,G ks11243057 chrM 13175 T C,T ks11243058 chrM 13183 T C,T ks11243059 chrM 13234 A A,G ks11243060 chrM 13240 C C,T ks11243061 chrM 13264 A A,G ks11243062 chrM 13438 T C,T ks11243063 chrM 13478 G A,G ks11243064 chrM 13652 A A,C,G ks11243065 chrM 13717 A A,G ks11243066 chrM 13929 G C,G ks11243067 chrM 13943 A A,G ks11243068 chrM 14149 A A,G ks11243069 chrM 14163 G A,G ks11243070 chrM 14199 G A,G ks11243071 chrM 14312 T C,T ks11243072 chrM 14319 T C,T ks11243073 chrM 14320 T C,T ks11243074 chrM 14341 C C,T ks11243075 chrM 14365 G A,G ks11243076 chrM 14456 C C,T ks11243077 chrM 14477 G A,G ks11243078 chrM 14531 T C,T ks11243079 chrM 14561 G A,G ks11243080 chrM 14570 G A,G ks11243081 chrM 14669 C C,T ks11243082 chrM 14784 T C,T ks11243083 chrM 14945 C C,T ks11243084 chrM 14979 A A,G ks11243085 chrM 14980 T C,T ks11243086 chrM 15023 C C,T ks11243087 chrM 15044 G A,G ks11243088 chrM 15068 T C,T ks11243089 chrM 15091 T C,T ks11243090 chrM 15140 T C,T ks11243091 chrM 15149 G A,G ks11243092 chrM 15173 G A,G ks11243093 chrM 15185 T C,T ks11243094 chrM 15224 C C,T ks11243095 chrM 15251 C C,T ks11243096 chrM 15302 A A,G ks11243097 chrM 15324 G A,G ks11243098 chrM 15460 C C,T ks11243099 chrM 15488 A A,T ks11243100 chrM 15498 G A,G ks11243101 chrM 15509 C C,T ks11243102 chrM 15519 C C,T ks11243103 chrM 15536 C C,T ks11243104 chrM 15663 A A,G ks11243105 chrM 15725 A A,G ks11243106 chrM 15735 G A,G ks11243107 chrM 15747 A A,G ks11243108 chrM 15774 G A,G ks11243109 chrM 15833 C C,T ks11243110 chrM 15851 T C,T ks11243111 chrM 15852 A A,G ks11243112 chrM 15861 A A,G ks11243113 chrM 15875 A A,G ks11243114 chrM 15928 G A,G ks11243115 chrM 15931 G A,G ks11243116 chrM 15955 A A,G ks11243117 chrM 16094 T C,T ks11243118 chrM 16112 C C,T ks11243119 chrM 16127 T C,T ks11243120 chrM 16130 G A,G ks11243121 chrM 16137 T C,T ks11243122 chrM 16141 T C,T ks11243123 chrM 16146 G A,G ks11243124 chrM 16151 C C,T ks11243125 chrM 16165 A A,G ks11243126 chrM 16168 C C,T ks11243127 chrM 16171 A A,G ks11243128 chrM 16173 C C,T ks11243129 chrM 16183 A A,C ks11243130 chrM 16185 C A,C ks11243131 chrM 16186 C C,T ks11243132 chrM 16188 C C,T ks11243133 chrM 16189 C C,T ks11243134 chrM 16191 C C,T ks11243135 chrM 16211 T C,T ks11243136 chrM 16219 T C,T ks11243137 chrM 16225 T C,T ks11243138 chrM 16234 C A,C ks11243139 chrM 16236 C C,T ks11243140 chrM 16245 T C,T ks11243141 chrM 16251 T C,T ks11243142 chrM 16258 C C,T ks11243143 chrM 16259 C A,C ks11243144 chrM 16263 C C,T ks11243145 chrM 16267 A A,C ks11243146 chrM 16268 C C,T ks11243147 chrM 16276 G A,G ks11243148 chrM 16280 C C,T ks11243149 chrM 16292 C C,T ks11243150 chrM 16293 C C,T ks11243151 chrM 16299 T C,T ks11243152 chrM 16300 T C,T ks11243153 chrM 16306 T C,T ks11243154 chrM 16313 T C,T ks11243155 chrM 16321 G A,G ks11243156 chrM 16326 T C,T ks11243157 chrM 16327 T C,T ks11243158 chrM 16329 C C,T ks11243159 chrM 16346 C C,T ks11243160 chrM 16357 C C,T ks11243161 chrM 16359 T C,T ks11243162 chrM 16364 T C,T ks11243163 chrM 16367 C C,T ks11243164 chrM 16465 A A,G ks11243165 chrM 16499 A A,G ks11243166 chrM 16521 C C,T ks11243167