diff --git a/README.md b/README.md index f7c55d9..7097eb8 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ for Multiple Tools [![codecov](https://codecov.io/gh/rhshah/basicfiltering/branch/master/graph/badge.svg)](https://codecov.io/gh/rhshah/basicfiltering) ## Requirements: -- pyvcf : [v0.6.8](http://pyvcf.readthedocs.io/en/latest/INTRO.html) +- pyvcf : [v0.6.7](http://pyvcf.readthedocs.io/en/latest/INTRO.html) - pandas : [v0.16.2](http://pandas.pydata.org/) - nose : [v1.3.7](http://nose.readthedocs.io/en/latest/) diff --git a/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf b/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf index a3e8736..58a20a1 100644 --- a/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf +++ b/data/sample_output/PoolTumor2-T_bc52_PINDEL_0.2.5a7_STDfilter.vcf @@ -13,6 +13,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= +##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PoolNormal-N PoolTumor2-T 2 6636086 . A AGCTTCGTTAAACTTCACTCGGAAGT . PASS END=6636086;HOMLEN=0;SVLEN=25;SVTYPE=INS GT:AD 0/0:554,1 0/0:719,10 2 29451557 . GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G . PASS END=29451604;HOMLEN=7;HOMSEQ=AGGCAGG;SVLEN=-47;SVTYPE=DEL GT:AD 0/0:59,0 0/0:145,5 diff --git a/data/sample_output/PoolTumor2-T_bc52_muTect_1.1.4_STDfilter.vcf b/data/sample_output/PoolTumor2-T_bc52_muTect_1.1.4_STDfilter.vcf index 381619a..432d294 100644 --- a/data/sample_output/PoolTumor2-T_bc52_muTect_1.1.4_STDfilter.vcf +++ b/data/sample_output/PoolTumor2-T_bc52_muTect_1.1.4_STDfilter.vcf @@ -5,6 +5,7 @@ ##INFO= ##INFO= ##INFO= +##INFO= ##FORMAT= ##FORMAT= ##FORMAT= @@ -101,1011 +102,1011 @@ ##contig= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PoolTumor2-T PoolNormal-N -1 4955833 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:128,12:30.0:140:0.086:2 0:179,0:.:179:0.0:0 -1 11181985 rs41274510 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:165,32:30.0:197:0.162:2 0:173,0:.:173:0.0:0 -1 11317260 . G A . PASS . GT:AD:BQ:DP:FA 0/1:194,5:29.0:200:0.025 0:217,0:.:217:0.0 -1 14192818 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:32,8:31.0:40:0.2:2 0:35,0:.:36:0.0:0 -1 16258302 rs113470169 A G . PASS DB GT:AD:BQ:DP:FA 0/1:276,215:32.0:492:0.438 0:537,22:.:559:0.039 -1 16972793 . T A . PASS . GT:AD:BQ:DP:FA 0/1:336,23:29.0:359:0.064 0:325,0:.:325:0.0 -1 16974817 rs199598697 C G . PASS DB GT:AD:BQ:DP:FA 0/1:543,247:31.0:791:0.313 0:794,20:.:815:0.025 -1 16975228 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:3451,138:30.0:3594:0.038:2 0:3270,1:.:3273:0.0003057:0 -1 17087395 . G A . PASS . GT:AD:BQ:DP:FA 0/1:3103,31:29.0:3136:0.009892 0:2283,4:.:2288:0.001749 -1 23880912 rs34671368 G A . PASS DB GT:AD:BQ:DP:FA 0/1:66,170:30.0:236:0.72 0:285,8:.:293:0.027 -1 23881005 rs35140318 G A . PASS DB GT:AD:BQ:DP:FA 0/1:209,639:31.0:848:0.754 0:1001,24:.:1025:0.023 -1 27533368 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:159,19:30.0:178:0.107:2 0:224,0:.:224:0.0:0 -1 36824305 rs145929365 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:439,74:30.0:513:0.144:2 0:480,0:.:481:0.0:0 -1 45798981 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:647,24:28.0:671:0.036:2 0:656,1:.:657:0.001522:0 -1 46509146 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:6,5:31.0:11:0.455:2 0:12,0:.:12:0.0:0 -1 46740500 rs75959881 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:79,8:32.0:87:0.092:2 0:77,0:.:77:0.0:0 -1 51436157 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:317,12:29.0:329:0.036:2 0:363,0:.:363:0.0:0 -1 51439777 rs1043141 C T . PASS DB GT:AD:BQ:DP:FA 0/1:301,63:30.0:364:0.173 0:404,11:.:416:0.027 -1 59250675 rs17265089 C G . PASS DB GT:AD:BQ:DP:FA 0/1:884,187:32.0:1073:0.175 0:1046,26:.:1072:0.024 -1 65321028 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,3:33.0:23:0.136:2 0:15,0:.:15:0.0:0 -1 65332766 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:475,20:30.0:497:0.04:2 0:476,0:.:476:0.0:0 -1 65349304 rs72675459 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:35,10:31.0:45:0.222:2 0:32,0:.:32:0.0:0 -1 65351748 rs112941888 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:47,7:31.0:54:0.13:2 0:47,0:.:47:0.0:0 -1 69777307 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:9,3:32.0:12:0.25:2 0:15,0:.:15:0.0:0 -1 72058827 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:43,6:31.0:49:0.122:2 0:34,0:.:34:0.0:0 -1 72748280 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:74,22:30.0:96:0.229:2 0:172,0:.:172:0.0:0 -1 84971819 rs76421103 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:16,5:28.0:21:0.238:2 0:22,0:.:22:0.0:0 -1 85739861 rs12563515 A G . PASS DB GT:AD:BQ:DP:FA 0/1:77,31:32.0:108:0.287 0:73,4:.:77:0.052 -1 85741968 rs12562182 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1005,50:32.0:1056:0.047:2 0:1248,0:.:1250:0.0:0 -1 85742157 rs1060843 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:229,10:30.0:242:0.042:2 0:227,0:.:227:0.0:0 -1 101971074 rs404156 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:36,11:30.0:47:0.234:2 0:52,0:.:52:0.0:0 -1 117753543 rs61759536 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:279,44:30.0:323:0.136:2 0:244,0:.:244:0.0:0 -1 118166096 rs2884587 C T . PASS DB GT:AD:BQ:DP:FA 0/1:709,150:30.0:859:0.175 0:701,19:.:722:0.026 -1 118166750 rs2066411 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:31,19:30.0:50:0.38:2 0:23,0:.:23:0.0:0 -1 120429402 rs74115384 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:72,5:33.0:77:0.065:2 0:51,0:.:51:0.0:0 -1 120468134 rs6692009 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:626,133:30.0:760:0.175:2 0:579,0:.:579:0.0:0 -1 120468487 rs6658796 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:98,29:29.0:127:0.228:2 0:127,0:.:128:0.0:0 -1 149857797 rs202141121 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:45,15:32.0:60:0.25:2 0:43,0:.:43:0.0:0 -1 152330829 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:147,65:30.0:212:0.307:2 0:112,0:.:112:0.0:0 -1 152331013 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:153,21:31.0:174:0.121:2 0:88,0:.:88:0.0:0 -1 156785653 . C G . PASS . GT:AD:BQ:DP:FA 0/1:875,31:32.0:910:0.034 0:636,0:.:637:0.0 -1 156848778 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:92,18:29.0:110:0.164:2 0:37,0:.:37:0.0:0 -1 156849047 rs142870382 G T . PASS DB GT:AD:BQ:DP:FA 0/1:987,20:30.0:1008:0.02 0:518,0:.:519:0.0 -1 156849658 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:89,11:31.0:100:0.11:2 0:26,0:.:26:0.0:0 -1 157599882 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:142,18:31.0:160:0.113:2 0:139,0:.:139:0.0:0 -1 162737241 rs75932087 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:149,18:29.0:167:0.108:2 0:68,0:.:68:0.0:0 -1 162740121 rs34722354 G A . PASS DB GT:AD:BQ:DP:FA 0/1:577,206:29.0:783:0.263 0:500,25:.:525:0.048 -1 165044147 rs34089781 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:38,53:31.0:91:0.582:2 0:59,0:.:59:0.0:0 -1 175958637 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:386,15:29.0:401:0.037:2 0:246,0:.:247:0.0:0 -1 176175885 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:176,10:31.0:186:0.054:2 0:102,0:.:102:0.0:0 -1 181819202 rs190395201 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:55,14:30.0:69:0.203:2 0:37,0:.:37:0.0:0 -1 184327323 rs6665185 T G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:159,60:31.0:219:0.274:2 0:107,0:.:108:0.0:0 -1 185520654 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:458,19:31.0:478:0.04:2 0:206,0:.:206:0.0:0 -1 193091490 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:579,16:30.0:596:0.027:2 0:313,0:.:313:0.0:0 -1 193104712 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:492,106:30.0:598:0.177:2 0:364,0:.:364:0.0:0 -1 193203268 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:381,19:30.0:402:0.048:2 0:221,0:.:222:0.0:0 -1 204495610 . G T . PASS . GT:AD:BQ:DP:FA 0/1:158,7:27.0:166:0.042 0:158,1:.:163:0.006289 -1 206648147 rs1953090 T G . PASS DB GT:AD:BQ:DP:FA 0/1:235,99:30.0:335:0.296 0:170,8:.:178:0.045 -1 206650065 rs41296034 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:589,200:32.0:789:0.253:2 0:530,0:.:530:0.0:0 -1 206944936 . T C . PASS . GT:AD:BQ:DP:FA 0/1:48,3:33.0:51:0.059 0:16,0:.:16:0.0 -1 221053574 rs62621984 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:67,5:33.0:72:0.069:2 0:61,0:.:61:0.0:0 -1 226562112 rs1805401 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:230,60:32.0:290:0.207:2 0:157,0:.:157:0.0:0 -1 226567172 rs2271345 A C . PASS DB GT:AD:BQ:DP:FA 0/1:171,57:30.0:228:0.25 0:116,6:.:123:0.049 -1 228617397 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:303,45:28.0:348:0.129:2 0:120,0:.:120:0.0:0 -1 230355441 rs12061439 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:227,79:30.0:306:0.258:2 0:200,0:.:200:0.0:0 -1 241663941 . C G . PASS . GT:AD:BQ:DP:FA 0/1:236,4:30.0:241:0.017 0:96,0:.:96:0.0 -1 247555079 rs114193294 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:25,11:32.0:36:0.306:2 0:20,0:.:20:0.0:0 -2 6636119 rs147273945 T A . PASS DB GT:AD:BQ:DP:FA 0/1:604,28:30.0:633:0.044 0:440,4:.:444:0.009009 -2 6636414 rs183255044 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:695,42:30.0:737:0.057:2 0:502,0:.:502:0.0:0 -2 6636735 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:479,18:30.0:498:0.036:2 0:318,0:.:318:0.0:0 -2 7541718 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:114,38:30.0:153:0.25:2 0:153,0:.:154:0.0:0 -2 14528089 rs147905894 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:285,33:30.0:319:0.104:2 0:221,0:.:222:0.0:0 -2 16085519 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:84,8:31.0:92:0.087:2 0:34,0:.:34:0.0:0 -2 25466810 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:745,27:30.0:773:0.035:2 0:616,0:.:619:0.0:0 -2 25972936 rs192716734 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:721,54:29.0:778:0.07:2 0:581,0:.:582:0.0:0 -2 27014885 rs143726653 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:166,10:27.0:176:0.057:2 0:108,0:.:108:0.0:0 -2 29429948 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:274,49:31.0:323:0.152:2 0:185,1:.:186:0.005376:0 -2 29451986 rs62130588 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:316,17:28.0:333:0.051:2 0:165,0:.:165:0.0:0 -2 29519851 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:810,36:31.0:846:0.043:2 0:649,1:.:651:0.001538:0 -2 29940332 rs116369425 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:84,12:31.0:96:0.125:2 0:51,0:.:51:0.0:0 -2 43952068 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:52,9:30.0:61:0.148:2 0:51,0:.:51:0.0:0 -2 46128526 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:289,32:31.0:321:0.1:2 0:173,0:.:174:0.0:0 -2 47630213 rs2303425 T C . PASS DB GT:AD:BQ:DP:FA 0/1:73,51:32.0:125:0.411 0:61,3:.:64:0.047 -2 47630314 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:404,32:31.0:436:0.073:2 0:328,0:.:328:0.0:0 -2 47693788 rs12998837 A T . PASS DB GT:AD:BQ:DP:FA 0/1:269,165:29.0:434:0.38 0:291,21:.:312:0.067 -2 47708075 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:125,31:30.0:157:0.199:2 0:111,0:.:111:0.0:0 -2 47709807 rs6737098 T A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:108,21:30.0:129:0.163:2 0:54,1:.:55:0.018:0 -2 47905398 rs182017009 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:459,125:29.0:584:0.214:2 0:537,1:.:538:0.001859:0 -2 48025764 rs1800937 C T . PASS DB GT:AD:BQ:DP:FA 0/1:262,97:31.0:359:0.27 0:361,18:.:379:0.047 -2 48030629 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:906,51:30.0:957:0.053:2 0:966,0:.:967:0.0:0 -2 51288710 rs34304690 A C . PASS DB GT:AD:BQ:DP:FA 0/1:545,378:32.0:924:0.41 0:639,44:.:683:0.064 -2 54660484 rs17045894 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:269,25:30.0:294:0.085:2 0:226,1:.:227:0.004405:0 -2 61108926 rs147771199 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:157,87:32.0:245:0.357:2 0:265,0:.:265:0.0:0 -2 61710320 rs113262337 T A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:86,6:32.0:92:0.065:2 0:68,0:.:68:0.0:0 -2 61760814 rs115819167 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:172,23:30.0:195:0.118:2 0:140,0:.:140:0.0:0 -2 67049381 rs61743348 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:298,58:31.0:356:0.163:2 0:208,0:.:208:0.0:0 -2 79524994 rs72917249 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:129,165:30.0:294:0.561:2 0:221,0:.:221:0.0:0 -2 81424759 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1231,153:31.0:1384:0.111:2 0:979,0:.:979:0.0:0 -2 81425558 . C T . PASS . GT:AD:BQ:DP:FA 0/1:1519,19:30.0:1539:0.012 0:1060,0:.:1062:0.0 -2 81425585 rs112215672 C T . PASS DB GT:AD:BQ:DP:FA 0/1:1033,462:30.0:1500:0.309 0:989,47:.:1037:0.045 -2 81426909 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1279,451:30.0:1732:0.261:2 0:1210,0:.:1213:0.0:0 -2 81427308 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:730,304:30.0:1034:0.294:2 0:714,0:.:714:0.0:0 -2 99160361 rs2230387 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:621,43:31.0:664:0.065:2 0:532,0:.:535:0.0:0 -2 106021437 rs72945057 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:234,38:31.0:272:0.14:2 0:217,0:.:217:0.0:0 -2 111881810 rs72948328 C T . PASS DB GT:AD:BQ:DP:FA 0/1:55,18:30.0:73:0.247 0:61,3:.:65:0.047 -2 111885565 rs116747219 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:140,37:31.0:177:0.209:2 0:162,0:.:162:0.0:0 -2 111909610 rs79493742 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:75,7:32.0:82:0.085:2 0:48,1:.:49:0.02:0 -2 113978894 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:290,140:30.0:431:0.326:2 0:340,1:.:342:0.002933:0 -2 113979364 rs72831810 G A . PASS DB GT:AD:BQ:DP:FA 0/1:328,57:30.0:385:0.148 0:315,7:.:322:0.022 -2 113981691 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:525,21:31.0:546:0.038:2 0:514,1:.:515:0.001942:0 -2 121735983 rs169430 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:214,18:29.0:232:0.078:2 0:195,0:.:195:0.0:0 -2 128038005 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:383,20:31.0:403:0.05:2 0:367,0:.:367:0.0:0 -2 131950767 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:227,99:32.0:326:0.304:2 0:265,0:.:265:0.0:0 -2 136869825 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:49,4:31.0:53:0.075:2 0:23,0:.:23:0.0:0 -2 158617379 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:807,197:31.0:1004:0.196:2 0:919,0:.:919:0.0:0 -2 158622572 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1313,113:30.0:1426:0.079:2 0:1094,1:.:1098:0.0009132:0 -2 158655838 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:232,19:32.0:251:0.076:2 0:177,0:.:177:0.0:0 -2 173914884 rs56306605 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:48,12:33.0:60:0.2:2 0:43,1:.:44:0.023:0 -2 180265135 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:381,68:31.0:449:0.151:2 0:439,0:.:439:0.0:0 -2 180265174 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:478,100:30.0:578:0.173:2 0:578,1:.:579:0.001727:0 -2 184373044 rs140832966 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:10,5:31.0:15:0.333:2 0:27,0:.:27:0.0:0 -2 189541807 rs7579655 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:35,13:32.0:48:0.271:2 0:38,0:.:38:0.0:0 -2 190708712 rs2066459 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:597,118:30.0:715:0.165:2 0:563,0:.:563:0.0:0 -2 190718940 rs5743137 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:137,64:32.0:201:0.318:2 0:190,0:.:190:0.0:0 -2 198257008 rs72912888 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:137,91:32.0:228:0.399:2 0:192,0:.:192:0.0:0 -2 198266602 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:376,29:30.0:406:0.072:2 0:378,0:.:379:0.0:0 -2 198285583 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:11,3:32.0:14:0.214:2 0:8,0:.:8:0.0:0 -2 202137781 rs200682299 C T . PASS DB GT:AD:BQ:DP:FA 0/1:63,8:17.0:71:0.113 0:71,5:.:76:0.066 -2 202149589 rs1045485 G C . PASS DB GT:AD:BQ:DP:FA 0/1:404,69:32.0:474:0.146 0:535,13:.:550:0.024 -2 212426588 rs139728050 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:319,34:30.0:353:0.096:2 0:390,0:.:391:0.0:0 -2 212522450 rs35497618 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:182,111:30.0:293:0.379:2 0:379,0:.:380:0.0:0 -2 212522651 rs34621071 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:350,145:31.0:495:0.293:2 0:560,0:.:560:0.0:0 -2 212578523 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:22,6:30.0:28:0.214:2 0:20,0:.:20:0.0:0 -2 212589774 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:218,18:32.0:236:0.076:2 0:258,0:.:258:0.0:0 -2 212698775 rs714394 T A . PASS DB GT:AD:BQ:DP:FA 0/1:95,95:31.0:190:0.5 0:160,11:.:171:0.064 -2 212812057 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:117,17:29.0:134:0.127:2 0:85,0:.:85:0.0:0 -2 225069340 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:154,14:30.0:168:0.083:2 0:156,0:.:156:0.0:0 -2 226701540 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:27,6:33.0:33:0.182:2 0:38,0:.:38:0.0:0 -3 12028100 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:18,4:30.0:22:0.182:2 0:8,0:.:8:0.0:0 -3 25569630 rs73048042 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:71,46:29.0:117:0.393:2 0:153,0:.:153:0.0:0 -3 29047705 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:94,9:31.0:103:0.087:2 0:138,0:.:138:0.0:0 -3 30713834 rs35766612 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:514,26:30.0:540:0.048:2 0:629,1:.:630:0.001587:0 -3 37034946 rs1800734 G A . PASS DB GT:AD:BQ:DP:FA 0/1:44,54:27.0:98:0.551 0:110,5:.:115:0.043 -3 37050254 rs4647255 T C . PASS DB GT:AD:BQ:DP:FA 0/1:106,60:31.0:166:0.361 0:149,5:.:154:0.032 -3 37061720 rs104894999 G C . PASS DB GT:AD:BQ:DP:FA 0/1:101,46:31.0:147:0.313 0:121,6:.:127:0.047 -3 41266226 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:402,23:32.0:426:0.054:2 0:424,0:.:425:0.0:0 -3 41275350 rs3856748 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:157,141:30.0:300:0.473:2 0:290,0:.:291:0.0:0 -3 41443220 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:248,13:31.0:261:0.05:2 0:288,0:.:288:0.0:0 -3 47061453 rs10510752 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:37,31:29.0:68:0.456:2 0:64,0:.:64:0.0:0 -3 47098278 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:179,55:32.0:234:0.235:2 0:222,1:.:224:0.004484:0 -3 48515221 rs187202071 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:9,9:30.0:18:0.5:2 0:29,0:.:29:0.0:0 -3 52436441 rs149499021 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:201,159:31.0:360:0.442:2 0:248,0:.:248:0.0:0 -3 52663084 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:125,14:31.0:139:0.101:2 0:173,0:.:173:0.0:0 -3 55487222 rs11709866 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:180,8:30.0:188:0.043:2 0:181,0:.:181:0.0:0 -3 69988437 . G T . PASS . GT:AD:BQ:DP:FA 0/1:40,6:20.0:46:0.13 0:42,0:.:42:0.0 -3 70005712 rs55754687 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:310,17:32.0:328:0.052:2 0:314,1:.:315:0.003175:0 -3 71007294 . G C . PASS . GT:AD:BQ:DP:FA 0/1:140,13:18.0:156:0.085 0:144,2:.:149:0.014 -3 71019797 rs139128497 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:93,51:31.0:144:0.354:2 0:182,0:.:182:0.0:0 -3 71246918 rs2293137 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:16,15:30.0:31:0.484:2 0:34,0:.:34:0.0:0 -3 71247014 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:185,7:32.0:192:0.036:2 0:214,0:.:214:0.0:0 -3 71247304 rs2037474 A G . PASS DB GT:AD:BQ:DP:FA 0/1:174,109:32.0:283:0.385 0:302,20:.:322:0.062 -3 72323080 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:132,17:31.0:149:0.114:2 0:199,0:.:199:0.0:0 -3 72323287 rs35092991 A G . PASS DB GT:AD:BQ:DP:FA 0/1:86,63:31.0:149:0.423 0:129,8:.:137:0.058 -3 75164938 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:40,38:28.0:78:0.487:2 0:105,0:.:105:0.0:0 -3 87347973 rs2646219 G T . PASS DB GT:AD:BQ:DP:FA 0/1:42,3:31.0:45:0.067 0:56,0:.:56:0.0 -3 89905902 rs58068122 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:63,36:31.0:99:0.364:2 0:84,0:.:84:0.0:0 -3 94429115 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:482,39:33.0:521:0.075:2 0:450,0:.:451:0.0:0 -3 106824274 rs16834059 G A . PASS DB GT:AD:BQ:DP:FA 0/1:122,86:30.0:208:0.413 0:178,7:.:185:0.038 -3 106824304 rs114734174 C T . PASS DB GT:AD:BQ:DP:FA 0/1:130,95:30.0:225:0.422 0:178,11:.:191:0.058 -3 106825024 rs7628252 G C . PASS DB GT:AD:BQ:DP:FA 0/1:138,140:31.0:278:0.504 0:239,20:.:259:0.077 -3 106825180 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:571,30:31.0:601:0.05:2 0:514,0:.:514:0.0:0 -3 117078556 rs116733551 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:24,5:34.0:29:0.172:2 0:34,0:.:34:0.0:0 -3 117078561 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:14,13:30.0:27:0.481:2 0:35,0:.:35:0.0:0 -3 128199913 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:478,161:30.0:641:0.252:2 0:428,0:.:428:0.0:0 -3 134670080 rs77546042 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:88,19:30.0:107:0.178:2 0:44,0:.:45:0.0:0 -3 134851577 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:548,70:31.0:618:0.113:2 0:482,0:.:482:0.0:0 -3 134884695 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:96,25:32.0:121:0.207:2 0:65,0:.:65:0.0:0 -3 134885042 rs9866044 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:91,40:32.0:131:0.305:2 0:58,0:.:58:0.0:0 -3 134967265 . G A . PASS . GT:AD:BQ:DP:FA 0/1:648,24:30.0:673:0.036 0:598,2:.:600:0.003333 -3 135644964 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:152,26:30.0:178:0.146:2 0:159,0:.:159:0.0:0 -3 137443260 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:29,5:27.0:34:0.147:2 0:37,0:.:37:0.0:0 -3 138374293 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:605,34:30.0:641:0.053:2 0:618,0:.:619:0.0:0 -3 138663179 rs2291251 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:399,183:32.0:582:0.314:2 0:556,0:.:557:0.0:0 -3 142188172 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:245,34:30.0:279:0.122:2 0:255,0:.:255:0.0:0 -3 142215149 rs74677466 T C . PASS DB GT:AD:BQ:DP:FA 0/1:111,31:32.0:142:0.218 0:89,3:.:92:0.033 -3 142215151 . T C . PASS . GT:AD:BQ:DP:FA 0/1:124,21:32.0:145:0.145 0:96,1:.:98:0.01 -3 142215153 . T C . PASS . GT:AD:BQ:DP:FA 0/1:140,5:32.0:145:0.034 0:103,0:.:103:0.0 -3 142218675 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:73,8:29.0:81:0.099:2 0:58,0:.:58:0.0:0 -3 142266439 rs13091637 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:23,30:30.0:53:0.566:2 0:28,0:.:28:0.0:0 -3 142278101 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:350,123:32.0:473:0.26:2 0:454,0:.:454:0.0:0 -3 178511531 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:251,15:29.0:266:0.056:2 0:219,0:.:219:0.0:0 -3 178927345 rs3729682 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:295,12:31.0:307:0.039:2 0:221,1:.:222:0.004505:0 -3 178936227 rs17849071 T G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:84,5:31.0:89:0.056:2 0:41,0:.:41:0.0:0 -3 185183491 rs192528458 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:214,97:30.0:311:0.312:2 0:277,0:.:277:0.0:0 -3 185183656 rs201265411 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:238,127:30.0:365:0.348:2 0:350,1:.:351:0.002849:0 -3 186504406 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:907,63:33.0:971:0.065:2 0:1005,0:.:1007:0.0:0 -3 187440126 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:61,6:26.0:67:0.09:2 0:37,0:.:38:0.0:0 -3 187451349 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:694,22:31.0:717:0.031:2 0:584,0:.:584:0.0:0 -3 189349501 rs13064999 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:56,54:31.0:110:0.491:2 0:70,1:.:71:0.014:0 -3 189525985 rs141006314 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:279,12:29.0:291:0.041:2 0:203,0:.:203:0.0:0 -3 189525986 rs149767941 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:283,12:31.0:295:0.041:2 0:207,0:.:207:0.0:0 -3 189584420 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:190,31:30.0:221:0.14:2 0:164,0:.:165:0.0:0 -3 189586466 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:369,18:30.0:387:0.047:2 0:333,0:.:334:0.0:0 -3 189586470 rs147148566 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:270,111:30.0:381:0.291:2 0:326,0:.:327:0.0:0 -3 189590871 rs111843185 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:147,52:30.0:199:0.261:2 0:124,0:.:125:0.0:0 -3 189597951 . G A . PASS . GT:AD:BQ:DP:FA 0/1:587,193:30.0:780:0.247 0:688,3:.:691:0.004342 -3 189598095 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:86,14:29.0:100:0.14:2 0:38,0:.:38:0.0:0 -3 195399620 rs9840981 C G . PASS DB GT:AD:BQ:DP:FA 0/1:187,153:32.0:341:0.45 0:113,22:.:135:0.163 -3 195399678 rs9874761 G T . PASS DB GT:AD:BQ:DP:FA 0/1:72,72:30.0:144:0.5 0:33,21:.:54:0.389 -3 195410875 rs201763651 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:163,53:28.0:216:0.245:2 0:74,0:.:74:0.0:0 -3 197346530 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:125,20:32.0:145:0.138:2 0:86,0:.:87:0.0:0 -4 1795762 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:442,39:30.0:481:0.081:2 0:317,1:.:318:0.003145:0 -4 1806937 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:85,21:31.0:107:0.198:2 0:35,0:.:35:0.0:0 -4 6113451 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:123,16:31.0:139:0.115:2 0:91,0:.:92:0.0:0 -4 20891334 . A T . PASS . GT:AD:BQ:DP:FA 0/1:38,3:31.0:41:0.073 0:21,0:.:21:0.0 -4 21650176 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:32,3:32.0:35:0.086:2 0:13,0:.:13:0.0:0 -4 28400468 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:132,26:31.0:158:0.165:2 0:113,0:.:113:0.0:0 -4 35861432 rs181017058 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:18,7:30.0:25:0.28:2 0:38,0:.:38:0.0:0 -4 41747691 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:14,4:32.0:18:0.222:2 0:13,0:.:13:0.0:0 -4 41748217 rs17885216 G A . PASS DB GT:AD:BQ:DP:FA 0/1:723,80:29.0:803:0.1 0:971,5:.:976:0.005123 -4 46726267 . C T . PASS . GT:AD:BQ:DP:FA 0/1:420,77:30.0:497:0.155 0:516,2:.:519:0.003861 -4 54245372 . T A . PASS . GT:AD:BQ:DP:FA 0/1:332,5:31.0:337:0.015 0:415,0:.:415:0.0 -4 55129831 rs55947416 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:281,196:30.0:478:0.411:2 0:471,0:.:471:0.0:0 -4 55138785 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:29,3:32.0:32:0.094:2 0:34,0:.:35:0.0:0 -4 55979609 . G A . PASS . GT:AD:BQ:DP:FA 0/1:532,41:30.0:573:0.072 0:622,2:.:624:0.003205 -4 65604620 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:85,43:29.0:128:0.336:2 0:115,0:.:115:0.0:0 -4 66189753 rs67487372 C T . PASS DB GT:AD:BQ:DP:FA 0/1:263,7:31.0:270:0.026 0:241,1:.:243:0.004132 -4 66218677 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:332,22:30.0:354:0.062:2 0:294,0:.:294:0.0:0 -4 66270345 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:36,7:31.0:43:0.163:2 0:14,0:.:14:0.0:0 -4 66286376 rs116596375 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:89,9:30.0:98:0.092:2 0:65,1:.:66:0.015:0 -4 78271554 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:180,10:32.0:191:0.053:2 0:201,0:.:202:0.0:0 -4 87163541 rs114515845 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:22,4:27.0:26:0.154:2 0:19,0:.:19:0.0:0 -4 120324304 . C T . PASS . GT:AD:BQ:DP:FA 0/1:69,8:30.0:77:0.104 0:76,0:.:76:0.0 -4 143043397 rs34561493 G A . PASS DB GT:AD:BQ:DP:FA 0/1:265,73:30.0:338:0.216 0:347,10:.:358:0.028 -4 143158979 rs28647625 A C . PASS DB GT:AD:BQ:DP:FA 0/1:106,82:31.0:188:0.436 0:162,3:.:165:0.018 -4 153245521 . C G . PASS . GT:AD:BQ:DP:FA 0/1:414,8:33.0:423:0.019 0:401,0:.:402:0.0 -4 166144830 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:269,22:32.0:291:0.076:2 0:337,0:.:337:0.0:0 -4 175047618 rs2196386 G A . PASS DB GT:AD:BQ:DP:FA 0/1:117,69:31.0:186:0.371 0:165,12:.:177:0.068 -4 182443933 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:206,30:32.0:236:0.127:2 0:371,0:.:371:0.0:0 -4 182444093 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:250,32:31.0:282:0.113:2 0:488,0:.:488:0.0:0 -4 182444132 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:125,75:31.0:200:0.375:2 0:338,1:.:340:0.00295:0 -4 187509875 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:281,45:30.0:326:0.138:2 0:436,0:.:436:0.0:0 -4 187527089 rs184407616 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:36,13:31.0:49:0.265:2 0:58,0:.:58:0.0:0 -4 187531022 rs28647489 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:344,101:31.0:445:0.227:2 0:537,1:.:538:0.001859:0 -4 187540042 rs192818736 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:479,52:30.0:531:0.098:2 0:642,1:.:643:0.001555:0 -4 187541598 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:409,13:29.0:422:0.031:2 0:450,0:.:450:0.0:0 -4 187542755 rs28489116 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:462,140:32.0:602:0.233:2 0:641,1:.:642:0.001558:0 -4 187542922 rs34360279 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:255,31:30.0:286:0.108:2 0:283,0:.:283:0.0:0 -4 187542986 rs28423024 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:85,34:32.0:119:0.286:2 0:107,0:.:107:0.0:0 -4 187557113 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:173,12:32.0:185:0.065:2 0:160,0:.:160:0.0:0 -4 187584530 rs200633985 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:452,54:30.0:506:0.107:2 0:470,1:.:472:0.002123:0 -4 187628352 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:190,81:30.0:271:0.299:2 0:329,0:.:330:0.0:0 -4 190093234 rs72727625 C T . PASS DB GT:AD:BQ:DP:FA 0/1:83,152:31.0:235:0.647 0:297,7:.:307:0.023 -5 240664 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:108,83:32.0:191:0.435:2 0:78,0:.:78:0.0:0 -5 1255297 rs113604559 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:152,13:30.0:165:0.079:2 0:50,0:.:50:0.0:0 -5 1272414 . G A . PASS . GT:AD:BQ:DP:FA 0/1:530,157:30.0:687:0.229 0:287,4:.:291:0.014 -5 1280190 rs147103794 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:338,97:30.0:435:0.223:2 0:164,0:.:164:0.0:0 -5 1293389 rs79662648 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:249,136:31.0:385:0.353:2 0:130,0:.:130:0.0:0 -5 1295250 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:644,199:29.0:845:0.236:2 0:368,0:.:369:0.0:0 -5 1576000 rs148387081 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:174,18:30.0:192:0.094:2 0:76,0:.:76:0.0:0 -5 17491448 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:332,99:28.0:431:0.23:2 0:221,0:.:221:0.0:0 -5 17670396 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:623,17:30.0:641:0.027:2 0:357,0:.:357:0.0:0 -5 22934638 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:89,6:28.0:95:0.063:2 0:55,0:.:55:0.0:0 -5 23303757 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:824,74:30.0:898:0.082:2 0:461,0:.:461:0.0:0 -5 23303943 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:800,44:30.0:844:0.052:2 0:434,0:.:434:0.0:0 -5 23304880 rs78261567 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:618,115:32.0:733:0.157:2 0:357,0:.:357:0.0:0 -5 26670194 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:195,12:29.0:207:0.058:2 0:65,0:.:65:0.0:0 -5 33997307 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:243,14:31.0:257:0.054:2 0:104,0:.:104:0.0:0 -5 35860873 rs148287783 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:109,51:29.0:160:0.319:2 0:97,0:.:97:0.0:0 -5 35871291 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:464,58:31.0:522:0.111:2 0:371,1:.:372:0.002688:0 -5 35875518 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:133,33:29.0:166:0.199:2 0:96,0:.:96:0.0:0 -5 38942628 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:49,6:32.0:55:0.109:2 0:22,0:.:22:0.0:0 -5 38947185 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:26,9:31.0:35:0.257:2 0:17,0:.:17:0.0:0 -5 38949632 rs116407384 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:116,36:29.0:152:0.237:2 0:68,0:.:68:0.0:0 -5 38962656 . T C . PASS . GT:AD:BQ:DP:FA 0/1:696,9:30.0:706:0.013 0:478,0:.:478:0.0 -5 40457488 rs112491400 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:385,20:30.0:405:0.049:2 0:255,1:.:256:0.003906:0 -5 52665368 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:215,10:31.0:225:0.044:2 0:212,0:.:212:0.0:0 -5 56168571 rs2053696 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:153,115:30.0:268:0.429:2 0:370,0:.:371:0.0:0 -5 62835420 rs13165927 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:22,9:32.0:31:0.29:2 0:39,1:.:40:0.025:0 -5 62836591 rs13153547 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:31,22:31.0:53:0.415:2 0:41,1:.:42:0.024:0 -5 62836726 rs13153708 T C . PASS DB GT:AD:BQ:DP:FA 0/1:159,142:30.0:302:0.472 0:329,9:.:339:0.027 -5 67569342 rs3730078 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:296,13:33.0:309:0.042:2 0:297,0:.:298:0.0:0 -5 79172158 rs77646428 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:170,20:30.0:190:0.105:2 0:156,0:.:156:0.0:0 -5 112043283 rs182500056 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:81,9:30.0:90:0.1:2 0:63,0:.:63:0.0:0 -5 112175617 rs67622085 T A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:550,67:30.0:619:0.109:2 0:825,1:.:828:0.001211:0 -5 112213686 . G C . PASS . GT:AD:BQ:DP:FA 0/1:221,6:28.0:228:0.026 0:369,0:.:370:0.0 -5 112227998 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:929,60:30.0:989:0.061:2 0:1057,1:.:1059:0.0009452:0 -5 140256920 rs115718636 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:118,158:32.0:276:0.572:2 0:236,0:.:237:0.0:0 -5 149460627 rs201114404 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:218,18:31.0:236:0.076:2 0:124,0:.:124:0.0:0 -5 149502838 rs56388645 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:96,114:30.0:210:0.543:2 0:91,0:.:91:0.0:0 -5 170828123 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:24,4:32.0:28:0.143:2 0:28,0:.:28:0.0:0 -5 176516631 rs1966265 G A . PASS DB GT:AD:BQ:DP:FA 0/1:403,131:31.0:534:0.245 0:542,2:.:544:0.003676 -5 176517801 rs55701137 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:846,36:31.0:882:0.041:2 0:688,0:.:688:0.0:0 -5 176524465 rs146820395 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:705,35:29.0:740:0.047:2 0:542,1:.:543:0.001842:0 -5 176636546 rs201076688 G A . PASS DB GT:AD:BQ:DP:FA 0/1:28,28:27.0:56:0.5 0:98,4:.:104:0.039 -5 176637149 rs3733874 G A . PASS DB GT:AD:BQ:DP:FA 0/1:102,223:30.0:325:0.686 0:344,10:.:354:0.028 -5 176637240 rs3733875 G T . PASS DB GT:AD:BQ:DP:FA 0/1:160,294:30.0:456:0.648 0:433,14:.:447:0.031 -5 176637576 rs28932178 T C . PASS DB GT:AD:BQ:DP:FA 0/1:132,220:32.0:352:0.625 0:333,11:.:344:0.032 -5 178996554 rs115920408 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:16,28:30.0:44:0.636:2 0:26,0:.:26:0.0:0 -5 180046427 rs141303558 C T . PASS DB GT:AD:BQ:DP:FA 0/1:300,7:29.0:307:0.023 0:222,1:.:223:0.004484 -5 180046494 . G C . PASS . GT:AD:BQ:DP:FA 0/1:4,6:32.0:10:0.6 0:102,2:.:105:0.019 -6 6728616 rs9504905 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:10,16:31.0:26:0.615:2 0:20,0:.:20:0.0:0 -6 20486794 rs3763279 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:61,7:28.0:68:0.103:2 0:46,0:.:46:0.0:0 -6 25261662 rs113389452 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:102,58:30.0:160:0.363:2 0:140,0:.:140:0.0:0 -6 25606672 rs742130 C T . PASS DB GT:AD:BQ:DP:FA 0/1:188,96:30.0:284:0.338 0:194,11:.:207:0.054 -6 26031720 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:61,14:31.0:76:0.187:2 0:36,0:.:36:0.0:0 -6 26322501 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:126,42:30.0:168:0.25:2 0:136,0:.:136:0.0:0 -6 27840221 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:194,13:31.0:207:0.063:2 0:125,0:.:125:0.0:0 -6 29236588 rs17344111 A G . PASS DB GT:AD:BQ:DP:FA 0/1:82,35:32.0:117:0.299 0:86,4:.:90:0.044 -6 29693183 rs150767875 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:227,94:30.0:321:0.293:2 0:240,0:.:241:0.0:0 -6 29760132 rs114179071 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:198,93:29.0:291:0.32:2 0:195,0:.:197:0.0:0 -6 29760317 rs61737605 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:102,36:31.0:138:0.261:2 0:103,0:.:103:0.0:0 -6 29760462 rs61729757 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:140,22:32.0:162:0.136:2 0:165,0:.:165:0.0:0 -6 29760765 rs115583841 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:331,90:30.0:421:0.214:2 0:374,0:.:374:0.0:0 -6 29760799 rs77141969 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:247,76:30.0:323:0.235:2 0:291,0:.:292:0.0:0 -6 29760856 rs116510017 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:133,65:29.0:198:0.328:2 0:128,0:.:128:0.0:0 -6 29769246 rs9468626 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:69,34:30.0:103:0.33:2 0:79,0:.:79:0.0:0 -6 29795566 rs17875397 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:292,117:29.0:409:0.286:2 0:261,1:.:262:0.003817:0 -6 29795913 rs41551813 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:318,121:31.0:439:0.276:2 0:263,0:.:263:0.0:0 -6 29796106 rs17875399 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:320,38:30.0:360:0.106:2 0:304,0:.:305:0.0:0 -6 29796265 rs17875401 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:91,38:30.0:129:0.295:2 0:53,0:.:53:0.0:0 -6 29796675 rs17875404 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:41,14:30.0:55:0.255:2 0:26,0:.:26:0.0:0 -6 29797155 rs17875405 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:171,81:31.0:252:0.321:2 0:166,0:.:166:0.0:0 -6 29797211 rs41562616 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:250,119:31.0:369:0.322:2 0:251,0:.:252:0.0:0 -6 29902040 rs1611306 A G . PASS DB GT:AD:BQ:DP:FA 0/1:148,37:31.0:185:0.2 0:109,32:.:141:0.227 -6 29910856 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:334,30:30.0:364:0.082:2 0:276,0:.:276:0.0:0 -6 29912149 rs114818671 G C . PASS DB GT:AD:BQ:DP:FA 0/1:910,241:31.0:1152:0.209 0:798,44:.:842:0.052 -6 29912852 rs1137296 T C . PASS DB GT:AD:BQ:DP:FA 0/1:635,113:32.0:748:0.151 0:382,214:.:597:0.359 -6 29925438 rs11757135 C T . PASS DB GT:AD:BQ:DP:FA 0/1:176,76:30.0:252:0.302 0:177,7:.:184:0.038 -6 30459165 rs62621992 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:321,33:31.0:354:0.093:2 0:335,0:.:335:0.0:0 -6 30670292 rs9405048 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:523,20:31.0:543:0.037:2 0:441,1:.:442:0.002262:0 -6 30672326 rs17292678 T C . PASS DB GT:AD:BQ:DP:FA 0/1:806,480:30.0:1286:0.373 0:990,60:.:1051:0.057 -6 30865204 rs2267641 A C . PASS DB GT:AD:BQ:DP:FA 0/1:54,14:33.0:68:0.206 0:71,3:.:74:0.041 -6 31238068 rs1050276 C T . PASS DB GT:AD:BQ:DP:FA 0/1:25,11:29.0:36:0.306 0:68,4:.:72:0.056 -6 31239050 rs713032 G T . PASS DB GT:AD:BQ:DP:FA 0/1:93,85:29.0:203:0.478 0:137,42:.:294:0.235 -6 31239602 rs1050441 G A . PASS DB GT:AD:BQ:DP:FA 0/1:182,53:30.0:235:0.226 0:330,23:.:353:0.065 -6 31322205 rs151341416 A C . PASS DB GT:AD:BQ:DP:FA 0/1:15,27:27.0:42:0.643 0:48,7:.:55:0.127 -6 31322209 rs9266106 A G . PASS DB GT:AD:BQ:DP:FA 0/1:15,19:23.0:39:0.559 0:41,0:.:59:0.0 -6 31323414 rs41563818 G A . PASS DB GT:AD:BQ:DP:FA 0/1:277,126:30.0:403:0.313 0:313,3:.:316:0.009494 -6 31324941 rs114038515 C T . PASS DB GT:AD:BQ:DP:FA 0/1:165,4:28.0:170:0.024 0:492,2:.:494:0.004049 -6 32188713 rs8192587 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:379,163:31.0:544:0.301:2 0:352,0:.:353:0.0:0 -6 32188823 rs8192585 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:443,245:30.0:689:0.356:2 0:484,0:.:484:0.0:0 -6 32189192 rs8192584 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:102,35:31.0:137:0.255:2 0:71,0:.:71:0.0:0 -6 32190484 rs8192569 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:255,470:31.0:725:0.648:2 0:552,1:.:555:0.001808:0 -6 33290827 . A T . PASS . GT:AD:BQ:DP:FA 0/1:102,5:30.0:107:0.047 0:66,0:.:66:0.0 -6 36650547 rs3176344 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:636,118:31.0:754:0.156:2 0:632,0:.:633:0.0:0 -6 43748328 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:82,56:31.0:140:0.406:2 0:63,0:.:63:0.0:0 -6 58777508 rs4388318 T G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:30,4:33.0:34:0.118:2 0:47,0:.:48:0.0:0 -6 58778828 rs28885508 T A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:25,6:32.0:31:0.194:2 0:48,1:.:49:0.02:0 -6 58779121 rs9500609 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:38,4:28.0:42:0.095:2 0:33,0:.:33:0.0:0 -6 90009220 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:168,14:29.0:182:0.077:2 0:158,0:.:158:0.0:0 -6 93973735 rs138667490 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:243,42:32.0:285:0.147:2 0:183,0:.:183:0.0:0 -6 93973784 . G T . PASS . GT:AD:BQ:DP:FA 0/1:127,6:24.0:133:0.045 0:61,0:.:61:0.0 -6 94066446 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1066,55:31.0:1121:0.049:2 0:950,1:.:951:0.001052:0 -6 94068208 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:303,22:32.0:325:0.068:2 0:240,0:.:240:0.0:0 -6 100498638 rs72942225 G T . PASS DB GT:AD:BQ:DP:FA 0/1:73,10:29.0:83:0.12 0:51,1:.:52:0.019 -6 100498976 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:113,24:31.0:137:0.175:2 0:138,0:.:138:0.0:0 -6 106051695 rs117032373 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:163,102:31.0:265:0.385:2 0:260,0:.:261:0.0:0 -6 106543620 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:207,46:30.0:253:0.182:2 0:249,1:.:250:0.004:0 -6 106553096 rs143040512 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:653,72:30.0:725:0.099:2 0:650,0:.:650:0.0:0 -6 117639262 rs9282844 G A . PASS DB GT:AD:BQ:DP:FA 0/1:205,20:29.0:225:0.089 0:162,2:.:164:0.012 -6 117648215 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1013,82:31.0:1096:0.075:2 0:854,0:.:856:0.0:0 -6 117652187 rs518987 T C . PASS DB GT:AD:BQ:DP:FA 0/1:65,39:30.0:104:0.375 0:69,3:.:72:0.042 -6 117662453 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:625,77:30.0:702:0.11:2 0:527,0:.:527:0.0:0 -6 117665115 rs76141666 G A . PASS DB GT:AD:BQ:DP:FA 0/1:52,35:30.0:87:0.402 0:44,2:.:46:0.043 -6 117707038 . G A . PASS . GT:AD:BQ:DP:FA 0/1:290,120:30.0:411:0.293 0:317,2:.:319:0.00627 -6 117724207 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:94,7:30.0:101:0.069:2 0:91,0:.:91:0.0:0 -6 131790227 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:40,4:29.0:44:0.091:2 0:54,0:.:54:0.0:0 -6 136295102 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:63,17:29.0:80:0.213:2 0:45,0:.:45:0.0:0 -6 137519780 rs3799488 T C . PASS DB GT:AD:BQ:DP:FA 0/1:127,94:30.0:221:0.425 0:213,9:.:222:0.041 -6 137539428 rs201357955 G A . PASS DB GT:AD:BQ:DP:FA 0/1:53,7:30.0:60:0.117 0:67,0:.:67:0.0 -6 137540536 rs17181457 G A . PASS DB GT:AD:BQ:DP:FA 0/1:132,63:30.0:195:0.323 0:122,5:.:127:0.039 -6 138027910 rs76195386 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:379,103:30.0:482:0.214:2 0:417,0:.:417:0.0:0 -6 138199768 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:577,242:31.0:820:0.295:2 0:828,0:.:829:0.0:0 -6 147728117 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:65,20:30.0:85:0.235:2 0:61,0:.:61:0.0:0 -6 148266586 rs12176381 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:20,35:31.0:55:0.636:2 0:42,1:.:44:0.023:0 -6 152164026 rs9340805 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:99,12:32.0:111:0.108:2 0:73,0:.:73:0.0:0 -6 152332921 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:437,41:32.0:479:0.086:2 0:392,0:.:394:0.0:0 -6 152333032 rs117509702 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:75,12:32.0:87:0.138:2 0:52,0:.:52:0.0:0 -6 157150230 rs12206233 A G . PASS DB GT:AD:BQ:DP:FA 0/1:61,31:29.0:92:0.337 0:47,2:.:49:0.041 -6 157511319 . G A . PASS . GT:AD:BQ:DP:FA 0/1:375,15:30.0:391:0.038 0:374,2:.:376:0.005319 -6 159215375 rs983208 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,3:31.0:22:0.136:2 0:23,0:.:23:0.0:0 -6 160640117 . A G . PASS . GT:AD:BQ:DP:FA 0/1:118,22:29.0:140:0.157 0:578,6:.:584:0.01 -6 161771037 rs62637702 T C . PASS DB GT:AD:BQ:DP:FA 0/1:122,44:30.0:166:0.265 0:211,9:.:220:0.041 -6 161771039 . T C . PASS . GT:AD:BQ:DP:FA 0/1:127,48:31.0:176:0.274 0:228,0:.:229:0.0 -6 162137107 . C A . PASS . GT:AD:BQ:DP:FA 0/1:785,72:30.0:857:0.084 0:801,2:.:804:0.002491 -6 162206873 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:429,64:31.0:494:0.13:2 0:534,0:.:534:0.0:0 -6 163528910 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:256,52:31.0:309:0.169:2 0:364,0:.:365:0.0:0 -6 169643879 rs73046003 T C . PASS DB GT:AD:BQ:DP:FA 0/1:78,38:31.0:116:0.328 0:46,2:.:48:0.042 -7 2166580 rs73037293 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:190,44:30.0:236:0.188:2 0:102,0:.:102:0.0:0 -7 2732378 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,3:31.0:22:0.136:2 0:11,0:.:11:0.0:0 -7 2951934 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:525,19:29.0:544:0.035:2 0:346,0:.:347:0.0:0 -7 2952915 rs199705831 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:512,17:29.0:529:0.032:2 0:231,0:.:231:0.0:0 -7 2962201 rs151225400 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:563,30:31.0:593:0.051:2 0:284,0:.:284:0.0:0 -7 2963744 rs190717725 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:182,12:32.0:194:0.062:2 0:53,0:.:53:0.0:0 -7 2968289 . T C . PASS . GT:AD:BQ:DP:FA 0/1:1127,20:30.0:1150:0.017 0:614,0:.:616:0.0 -7 2969660 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1092,55:29.0:1147:0.048:2 0:560,0:.:560:0.0:0 -7 2977768 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:148,7:30.0:156:0.045:2 0:90,0:.:90:0.0:0 -7 2985351 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:232,8:30.0:240:0.033:2 0:116,0:.:116:0.0:0 -7 6026530 rs1805324 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1169,68:29.0:1238:0.055:2 0:758,0:.:758:0.0:0 -7 6426892 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:756,35:31.0:792:0.044:2 0:517,1:.:519:0.001931:0 -7 6426908 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:680,56:31.0:737:0.076:2 0:494,0:.:495:0.0:0 -7 6438388 rs118039194 C T . PASS DB GT:AD:BQ:DP:FA 0/1:663,14:31.0:679:0.021 0:412,0:.:413:0.0 -7 6441993 rs61753123 C G . PASS DB GT:AD:BQ:DP:FA 0/1:621,15:31.0:637:0.024 0:477,0:.:479:0.0 -7 14026421 rs183005358 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:100,15:30.0:115:0.13:2 0:48,0:.:48:0.0:0 -7 14028575 rs187768235 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:550,74:30.0:625:0.119:2 0:384,0:.:384:0.0:0 -7 36859286 rs116070280 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:39,9:32.0:48:0.188:2 0:26,0:.:26:0.0:0 -7 39836727 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:124,12:30.0:136:0.088:2 0:45,0:.:45:0.0:0 -7 41729758 . C A . PASS . GT:AD:BQ:DP:FA 0/1:1907,26:30.0:1935:0.013 0:1102,2:.:1105:0.001812 -7 41729759 . A G . PASS . GT:AD:BQ:DP:FA 0/1:1912,24:30.0:1937:0.012 0:1099,1:.:1102:0.0009091 -7 41730289 rs80087315 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:157,44:31.0:201:0.219:2 0:70,0:.:70:0.0:0 -7 43299616 rs9639872 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,16:33.0:35:0.457:2 0:43,0:.:43:0.0:0 -7 47092291 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:164,18:31.0:182:0.099:2 0:51,0:.:51:0.0:0 -7 50455179 . C A . PASS . GT:AD:BQ:DP:FA 0/1:368,7:31.0:375:0.019 0:217,0:.:218:0.0 -7 53854866 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:539,15:31.0:554:0.027:2 0:308,0:.:308:0.0:0 -7 55222593 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:566,19:30.0:586:0.032:2 0:249,0:.:250:0.0:0 -7 55228160 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:88,30:32.0:118:0.254:2 0:27,0:.:27:0.0:0 -7 56430693 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:51,4:31.0:55:0.073:2 0:23,0:.:23:0.0:0 -7 56430843 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:116,7:32.0:123:0.057:2 0:57,0:.:57:0.0:0 -7 56432708 rs116729273 T C . PASS DB GT:AD:BQ:DP:FA 0/1:4,67:33.0:71:0.944 0:27,11:.:38:0.289 -7 56432714 rs114688169 C A . PASS DB GT:AD:BQ:DP:FA 0/1:4,67:30.0:71:0.944 0:22,11:.:33:0.333 -7 57228283 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:23,4:29.0:27:0.148:2 0:17,0:.:17:0.0:0 -7 63230653 rs113079374 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:62,10:30.0:72:0.139:2 0:49,1:.:50:0.02:0 -7 65970787 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:586,31:31.0:617:0.05:2 0:494,0:.:494:0.0:0 -7 70859670 rs73700929 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:33,5:31.0:38:0.132:2 0:33,0:.:33:0.0:0 -7 81336535 rs5745745 C A . PASS DB GT:AD:BQ:DP:FA 0/1:263,97:30.0:360:0.269 0:224,12:.:236:0.051 -7 81340916 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:164,11:30.0:175:0.063:2 0:116,0:.:116:0.0:0 -7 81388001 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:731,46:29.0:779:0.059:2 0:573,1:.:574:0.001742:0 -7 92404285 rs3731302 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:45,6:32.0:52:0.118:2 0:20,0:.:20:0.0:0 -7 103275947 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:53,7:32.0:60:0.117:2 0:38,0:.:38:0.0:0 -7 106522693 . G A . PASS . GT:AD:BQ:DP:FA 0/1:359,144:31.0:503:0.286 0:357,3:.:362:0.008333 -7 116339672 rs35775721 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:415,14:29.0:429:0.033:2 0:380,0:.:380:0.0:0 -7 116397572 rs13223756 A G . PASS DB GT:AD:BQ:DP:FA 0/1:482,245:32.0:727:0.337 0:648,14:.:662:0.021 -7 116403127 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:340,10:30.0:350:0.029:2 0:284,0:.:284:0.0:0 -7 116411923 rs34589476 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:426,69:30.0:495:0.139:2 0:415,0:.:415:0.0:0 -7 116423161 rs2073560 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,8:29.0:27:0.296:2 0:19,0:.:19:0.0:0 -7 128766971 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:461,22:30.0:483:0.046:2 0:504,1:.:505:0.00198:0 -7 128767250 rs61740497 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:568,141:30.0:710:0.199:2 0:580,0:.:581:0.0:0 -7 128829066 rs41304185 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:42,5:33.0:47:0.106:2 0:66,0:.:67:0.0:0 -7 128845223 rs111482521 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:280,60:31.0:340:0.176:2 0:288,0:.:288:0.0:0 -7 128849078 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:404,55:30.0:459:0.12:2 0:424,0:.:424:0.0:0 -7 128850084 rs4728158 T G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:36,39:29.0:75:0.52:2 0:53,1:.:54:0.019:0 -7 128851674 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:240,11:32.0:251:0.044:2 0:180,0:.:181:0.0:0 -7 128852381 rs2075780 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:47,34:30.0:81:0.42:2 0:52,1:.:53:0.019:0 -7 135335822 rs73721607 C T . PASS DB GT:AD:BQ:DP:FA 0/1:108,32:30.0:140:0.229 0:116,3:.:119:0.025 -7 140453136 rs113488022 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:338,58:31.0:396:0.146:2 0:441,0:.:441:0.0:0 -7 140482427 rs1267642 T C . PASS DB GT:AD:BQ:DP:FA 0/1:322,152:32.0:474:0.321 0:372,12:.:384:0.031 -7 140483403 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:374,146:31.0:520:0.281:2 0:458,0:.:459:0.0:0 -7 140483605 rs1267644 C T . PASS DB GT:AD:BQ:DP:FA 0/1:319,128:30.0:447:0.286 0:376,14:.:392:0.036 -7 140486743 rs1270193 T C . PASS DB GT:AD:BQ:DP:FA 0/1:549,199:32.0:749:0.266 0:851,28:.:883:0.032 -7 140487494 rs117001169 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:540,98:29.0:639:0.154:2 0:584,0:.:585:0.0:0 -7 140488156 rs1267633 T G . PASS DB GT:AD:BQ:DP:FA 0/1:302,137:32.0:439:0.312 0:393,18:.:411:0.044 -7 140489173 rs145359047 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:910,46:32.0:956:0.048:2 0:936,0:.:937:0.0:0 -7 140492039 rs1267636 T C . PASS DB GT:AD:BQ:DP:FA 0/1:398,169:32.0:567:0.298 0:455,13:.:468:0.028 -7 140494413 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:440,69:32.0:509:0.136:2 0:544,0:.:544:0.0:0 -7 140496563 rs1639675 T C . PASS DB GT:AD:BQ:DP:FA 0/1:400,188:32.0:589:0.32 0:489,15:.:504:0.03 -7 140497586 rs73491871 A T . PASS DB GT:AD:BQ:DP:FA 0/1:342,164:31.0:506:0.324 0:384,17:.:401:0.042 -7 140507901 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:261,24:30.0:286:0.084:2 0:268,0:.:269:0.0:0 -7 151168756 . G A . PASS . GT:AD:BQ:DP:FA 0/1:347,84:30.0:432:0.195 0:328,2:.:331:0.006061 -7 151828793 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:32,10:31.0:42:0.238:2 0:34,0:.:34:0.0:0 -7 151836397 rs149140699 T C . PASS DB GT:AD:BQ:DP:FA 0/1:167,6:25.0:174:0.035 0:163,0:.:164:0.0 -7 151874581 rs149373512 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:418,91:32.0:510:0.179:2 0:500,0:.:500:0.0:0 -7 151875047 rs117187677 G A . PASS DB GT:AD:BQ:DP:FA 0/1:274,65:30.0:339:0.192 0:326,3:.:330:0.009119 -7 151891255 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:458,96:30.0:555:0.173:2 0:530,1:.:532:0.001883:0 -7 151946985 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:458,18:32.0:477:0.038:2 0:526,0:.:526:0.0:0 -7 151949735 rs77652527 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:388,226:32.0:614:0.368:2 0:574,0:.:577:0.0:0 -7 152373367 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:28,4:29.0:32:0.125:2 0:41,0:.:41:0.0:0 -7 153622478 rs113821224 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:344,25:30.0:369:0.068:2 0:277,0:.:278:0.0:0 -7 153622749 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:165,10:28.0:175:0.057:2 0:162,0:.:162:0.0:0 -7 154594008 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:108,9:30.0:117:0.077:2 0:85,0:.:85:0.0:0 -7 154594127 rs192817693 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:106,29:29.0:135:0.215:2 0:95,0:.:95:0.0:0 -7 155835626 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:230,9:32.0:239:0.038:2 0:154,0:.:155:0.0:0 -7 158451102 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:51,9:33.0:60:0.15:2 0:34,0:.:34:0.0:0 -8 2387994 rs17693045 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:88,30:30.0:118:0.254:2 0:185,0:.:185:0.0:0 -8 3489674 rs6996858 G A . PASS DB GT:AD:BQ:DP:FA 0/1:63,23:30.0:87:0.267 0:116,5:.:121:0.041 -8 3489677 rs6983641 T C . PASS DB GT:AD:BQ:DP:FA 0/1:63,25:31.0:88:0.284 0:121,5:.:126:0.04 -8 3489842 rs6998329 C T . PASS DB GT:AD:BQ:DP:FA 0/1:59,33:29.0:92:0.359 0:112,4:.:116:0.034 -8 5498584 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:18,3:29.0:21:0.143:2 0:10,0:.:10:0.0:0 -8 11096235 rs17153021 G T . PASS DB GT:AD:BQ:DP:FA 0/1:107,19:29.0:127:0.151 0:115,3:.:119:0.025 -8 11587234 rs11250159 G T . PASS DB GT:AD:BQ:DP:FA 0/1:89,42:31.0:131:0.321 0:218,7:.:226:0.031 -8 14166427 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,3:31.0:22:0.136:2 0:17,0:.:17:0.0:0 -8 14166825 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:248,132:30.0:380:0.347:2 0:561,0:.:562:0.0:0 -8 23548530 rs117285286 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:759,78:31.0:838:0.093:2 0:1096,0:.:1098:0.0:0 -8 29496868 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:118,16:31.0:134:0.119:2 0:122,0:.:122:0.0:0 -8 38279065 rs181303271 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:30,13:28.0:43:0.302:2 0:22,0:.:22:0.0:0 -8 38283759 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:331,37:30.0:370:0.101:2 0:459,0:.:459:0.0:0 -8 38297776 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:191,24:32.0:216:0.112:2 0:347,0:.:347:0.0:0 -8 55371474 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:37,5:29.0:42:0.119:2 0:34,0:.:34:0.0:0 -8 55374948 rs75598791 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:259,22:30.0:281:0.078:2 0:265,0:.:265:0.0:0 -8 59337497 . G C . PASS . GT:AD:BQ:DP:FA 0/1:150,74:32.0:224:0.33 0:140,0:.:140:0.0 -8 59339186 rs17261333 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:339,83:30.0:423:0.197:2 0:435,0:.:437:0.0:0 -8 70250559 rs183747339 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:25,5:30.0:30:0.167:2 0:25,0:.:25:0.0:0 -8 74885277 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:43,6:31.0:49:0.122:2 0:34,0:.:34:0.0:0 -8 90958341 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:279,23:29.0:302:0.076:2 0:257,0:.:257:0.0:0 -8 91434037 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:118,6:29.0:124:0.048:2 0:84,0:.:84:0.0:0 -8 109144106 . C T . PASS . GT:AD:BQ:DP:FA 0/1:31,5:28.0:36:0.139 0:25,0:.:25:0.0 -8 109735723 rs141694956 T C . PASS DB GT:AD:BQ:DP:FA 0/1:99,28:32.0:127:0.22 0:100,2:.:102:0.02 -8 117864369 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:568,80:31.0:648:0.123:2 0:378,0:.:379:0.0:0 -8 125875063 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:199,53:30.0:252:0.21:2 0:103,0:.:103:0.0:0 -8 128747953 rs3824120 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:253,41:31.0:294:0.139:2 0:153,0:.:153:0.0:0 -8 128751201 rs2070582 G A . PASS DB GT:AD:BQ:DP:FA 0/1:463,83:29.0:547:0.152 0:361,3:.:364:0.008242 -8 145736791 rs201586678 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:547,448:31.0:997:0.45:2 0:329,0:.:329:0.0:0 -8 145738441 rs200114521 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:517,528:30.0:1046:0.505:2 0:357,0:.:357:0.0:0 -9 1011900 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:13,3:31.0:16:0.188:2 0:11,0:.:11:0.0:0 -9 2039827 rs10964525 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:16,15:31.0:31:0.484:2 0:29,0:.:29:0.0:0 -9 5126742 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:356,39:31.0:395:0.099:2 0:441,0:.:441:0.0:0 -9 5456083 rs72705424 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:284,21:31.0:305:0.069:2 0:367,0:.:367:0.0:0 -9 8331548 rs76379489 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:399,32:31.0:431:0.074:2 0:507,0:.:507:0.0:0 -9 16206756 rs58804257 T G . PASS DB GT:AD:BQ:DP:FA 0/1:108,76:32.0:185:0.413 0:229,3:.:233:0.013 -9 20776854 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:78,24:31.0:102:0.235:2 0:100,0:.:100:0.0:0 -9 21993964 rs2811711 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:39,39:31.0:78:0.5:2 0:65,0:.:65:0.0:0 -9 22012051 rs13298881 T C . PASS DB GT:AD:BQ:DP:FA 0/1:233,122:32.0:355:0.344 0:399,24:.:423:0.057 -9 33676618 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:309,19:31.0:329:0.058:2 0:385,1:.:387:0.002591:0 -9 80646091 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:597,38:30.0:635:0.06:2 0:710,0:.:711:0.0:0 -9 80795416 rs60126017 T C . PASS DB GT:AD:BQ:DP:FA 0/1:67,37:33.0:104:0.356 0:114,12:.:126:0.095 -9 87570478 . C A . PASS . GT:AD:BQ:DP:FA 0/1:411,61:31.0:473:0.129 0:487,2:.:490:0.00409 -9 93607915 rs114502181 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:279,49:30.0:328:0.149:2 0:255,0:.:256:0.0:0 -9 93636431 rs290228 A G . PASS DB GT:AD:BQ:DP:FA 0/1:322,233:32.0:555:0.42 0:510,31:.:542:0.057 -9 93641193 rs34231418 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:425,27:30.0:453:0.06:2 0:446,0:.:447:0.0:0 -9 93641199 rs2306040 T C . PASS DB GT:AD:BQ:DP:FA 0/1:276,156:32.0:432:0.361 0:410,20:.:431:0.047 -9 98009794 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:424,21:33.0:447:0.047:2 0:427,0:.:428:0.0:0 -9 98270324 rs28475503 A T . PASS DB GT:AD:BQ:DP:FA 0/1:91,5:24.0:96:0.052 0:90,0:.:91:0.0 -9 109484504 rs62567831 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:16,24:32.0:40:0.6:2 0:23,0:.:23:0.0:0 -9 133750550 rs35222907 A G . PASS DB GT:AD:BQ:DP:FA 0/1:80,39:32.0:120:0.328 0:115,2:.:117:0.017 -9 133759957 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:617,43:30.0:662:0.065:2 0:639,0:.:640:0.0:0 -9 135771515 rs116917669 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:50,39:29.0:89:0.438:2 0:56,1:.:57:0.018:0 -9 135782026 rs7870151 C A . PASS DB GT:AD:BQ:DP:FA 0/1:121,88:30.0:209:0.421 0:190,9:.:199:0.045 -9 135782221 rs7862221 T C . PASS DB GT:AD:BQ:DP:FA 0/1:213,182:32.0:395:0.461 0:322,24:.:346:0.069 -9 135786112 rs6597586 T C . PASS DB GT:AD:BQ:DP:FA 0/1:260,157:30.0:417:0.376 0:278,22:.:300:0.073 -9 135796608 rs17408598 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:40,28:31.0:68:0.412:2 0:46,1:.:47:0.021:0 -9 139391461 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:567,49:32.0:616:0.08:2 0:458,0:.:459:0.0:0 -9 139396113 rs11574906 T A . PASS DB GT:AD:BQ:DP:FA 0/1:100,84:29.0:184:0.457 0:90,7:.:97:0.072 -9 139397557 rs34383263 C G . PASS DB GT:AD:BQ:DP:FA 0/1:426,303:32.0:729:0.416 0:530,38:.:569:0.067 -9 139399641 rs13300218 G A . PASS DB GT:AD:BQ:DP:FA 0/1:104,76:30.0:180:0.422 0:89,5:.:94:0.053 -9 139401646 rs11574902 T C . PASS DB GT:AD:BQ:DP:FA 0/1:107,67:32.0:174:0.385 0:90,4:.:94:0.043 -9 139408892 rs3812609 C T . PASS DB GT:AD:BQ:DP:FA 0/1:11,128:29.0:139:0.921 0:56,3:.:59:0.051 -9 139412182 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:255,186:30.0:441:0.422:2 0:326,0:.:326:0.0:0 -9 139413908 rs2229975 C T . PASS DB GT:AD:BQ:DP:FA 0/1:407,293:30.0:701:0.419 0:505,2:.:507:0.003945 -9 139637329 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:35,4:32.0:39:0.103:2 0:47,0:.:47:0.0:0 -10 8100647 rs2229359 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:677,27:31.0:704:0.038:2 0:709,0:.:710:0.0:0 -10 8116079 rs2229360 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,40:30.0:59:0.678:2 0:28,0:.:28:0.0:0 -10 43596241 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:81,82:29.0:163:0.503:2 0:122,0:.:122:0.0:0 -10 43607471 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:112,12:31.0:124:0.097:2 0:87,0:.:87:0.0:0 -10 70406518 rs72799516 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:272,247:30.0:519:0.476:2 0:593,0:.:594:0.0:0 -10 70451383 rs183627556 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:636,102:28.0:739:0.138:2 0:920,0:.:920:0.0:0 -10 89692844 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:258,175:30.0:434:0.404:2 0:464,0:.:466:0.0:0 -10 123240645 rs3135821 C T . PASS DB GT:AD:BQ:DP:FA 0/1:331,292:30.0:624:0.469 0:629,48:.:678:0.071 -10 123241323 rs2912798 G A . PASS DB GT:AD:BQ:DP:FA 0/1:344,184:30.0:528:0.348 0:1098,51:.:1151:0.044 -10 123242589 rs2912797 G A . PASS DB GT:AD:BQ:DP:FA 0/1:168,125:30.0:293:0.427 0:284,16:.:300:0.053 -10 123274653 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:388,28:32.0:416:0.067:2 0:467,0:.:468:0.0:0 -11 2156741 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:656,100:32.0:756:0.132:2 0:691,0:.:691:0.0:0 -11 8248574 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:595,55:31.0:650:0.085:2 0:656,0:.:660:0.0:0 -11 17024886 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1,4:31.0:5:0.8:2 0:9,0:.:9:0.0:0 -11 17746976 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:829,33:30.0:862:0.038:2 0:810,0:.:810:0.0:0 -11 20575654 rs72938195 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:48,32:30.0:80:0.4:2 0:76,1:.:77:0.013:0 -11 21635295 rs56323531 T G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:139,72:31.0:212:0.341:2 0:198,0:.:198:0.0:0 -11 32437841 rs5030212 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,14:31.0:33:0.424:2 0:25,0:.:25:0.0:0 -11 32439001 rs5030198 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:67,40:31.0:107:0.374:2 0:85,0:.:85:0.0:0 -11 32452003 . A G . PASS . GT:AD:BQ:DP:FA 0/1:74,11:28.0:85:0.129 0:187,2:.:189:0.011 -11 39894274 rs11035553 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:72,41:31.0:113:0.363:2 0:126,0:.:126:0.0:0 -11 42138434 rs147928519 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:39,42:30.0:81:0.519:2 0:72,0:.:72:0.0:0 -11 64571710 . C T . PASS . GT:AD:BQ:DP:FA 0/1:371,6:29.0:377:0.016 0:339,0:.:339:0.0 -11 64575505 rs607969 C T . PASS DB GT:AD:BQ:DP:FA 0/1:559,67:31.0:627:0.107 0:676,2:.:681:0.00295 -11 69631013 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:292,37:30.0:330:0.112:2 0:205,0:.:206:0.0:0 -11 81185242 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:106,8:30.0:114:0.07:2 0:145,0:.:145:0.0:0 -11 85980945 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:62,5:32.0:67:0.075:2 0:52,0:.:52:0.0:0 -11 94203801 . C A . PASS . GT:AD:BQ:DP:FA 0/1:303,27:31.0:330:0.082 0:335,2:.:337:0.005935 -11 94770943 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:422,35:28.0:458:0.077:2 0:325,0:.:325:0.0:0 -11 100999043 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1087,88:30.0:1177:0.075:2 0:855,0:.:856:0.0:0 -11 100999194 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1040,90:30.0:1132:0.08:2 0:881,0:.:882:0.0:0 -11 108115594 . C T . PASS . GT:AD:BQ:DP:FA 0/1:610,13:31.0:623:0.021 0:611,0:.:612:0.0 -11 108143456 rs1800057 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:547,229:31.0:778:0.295:2 0:634,1:.:635:0.001575:0 -11 108160632 rs184920614 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:26,30:30.0:56:0.536:2 0:46,1:.:47:0.021:0 -11 108225473 rs139490310 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:242,12:30.0:254:0.047:2 0:208,0:.:209:0.0:0 -11 118307774 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:43,4:26.0:47:0.085:2 0:20,0:.:20:0.0:0 -11 118342819 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:672,17:31.0:689:0.025:2 0:516,0:.:518:0.0:0 -11 118370615 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:379,11:32.0:391:0.028:2 0:363,0:.:363:0.0:0 -11 118372452 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:926,83:32.0:1012:0.082:2 0:960,0:.:962:0.0:0 -11 123606029 rs6590005 A C . PASS DB GT:AD:BQ:DP:FA 0/1:82,73:32.0:155:0.471 0:135,10:.:145:0.069 -12 401969 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1187,33:28.0:1221:0.027:2 0:786,0:.:786:0.0:0 -12 406427 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:236,28:30.0:264:0.106:2 0:121,0:.:121:0.0:0 -12 416764 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:876,68:30.0:944:0.072:2 0:582,0:.:582:0.0:0 -12 459805 . C A . PASS . GT:AD:BQ:DP:FA 0/1:1203,20:29.0:1223:0.016 0:731,0:.:732:0.0 -12 465673 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:781,72:33.0:853:0.084:2 0:635,0:.:636:0.0:0 -12 1022352 rs11571475 A G . PASS DB GT:AD:BQ:DP:FA 0/1:44,25:33.0:69:0.362 0:30,1:.:32:0.032 -12 1038854 rs11571424 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:140,25:31.0:165:0.152:2 0:48,0:.:48:0.0:0 -12 9848467 rs11052489 T A . PASS DB GT:AD:BQ:DP:FA 0/1:109,52:31.0:161:0.323 0:155,13:.:168:0.077 -12 12006544 rs17210957 G A . PASS DB GT:AD:BQ:DP:FA 0/1:670,136:31.0:808:0.169 0:717,2:.:720:0.002782 -12 12009741 rs2238126 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:953,200:32.0:1156:0.173:2 0:1002,0:.:1002:0.0:0 -12 12016089 rs2238131 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1258,97:31.0:1357:0.072:2 0:1336,0:.:1339:0.0:0 -12 12018392 rs76197219 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:904,179:31.0:1083:0.165:2 0:999,0:.:999:0.0:0 -12 12018911 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1320,74:31.0:1394:0.053:2 0:1138,0:.:1139:0.0:0 -12 12022533 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:578,364:30.0:943:0.386:2 0:814,0:.:816:0.0:0 -12 12029765 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:346,59:32.0:406:0.146:2 0:315,0:.:315:0.0:0 -12 12031265 rs150206595 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:244,45:30.0:289:0.156:2 0:290,0:.:290:0.0:0 -12 12873211 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:65,5:30.0:70:0.071:2 0:60,0:.:60:0.0:0 -12 13767996 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:9,3:30.0:12:0.25:2 0:11,0:.:11:0.0:0 -12 16753747 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:117,21:29.0:138:0.152:2 0:91,0:.:92:0.0:0 -12 18467122 rs143458306 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:37,66:32.0:103:0.641:2 0:51,0:.:51:0.0:0 -12 18524061 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:291,18:32.0:309:0.058:2 0:239,0:.:239:0.0:0 -12 18690977 rs11044171 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:41,13:28.0:54:0.241:2 0:53,0:.:53:0.0:0 -12 18715728 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:370,31:32.0:402:0.077:2 0:659,0:.:660:0.0:0 -12 21600952 rs11046061 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:23,8:26.0:31:0.258:2 0:59,1:.:61:0.017:0 -12 25398285 rs121913530 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:649,82:30.0:731:0.112:2 0:461,0:.:461:0.0:0 -12 27578740 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:12,13:28.0:25:0.52:2 0:11,0:.:11:0.0:0 -12 38601111 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:28,7:26.0:35:0.2:2 0:24,0:.:24:0.0:0 -12 43131208 rs10506217 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:10,22:31.0:32:0.688:2 0:37,1:.:38:0.026:0 -12 46254505 rs183616884 C G . PASS DB GT:AD:BQ:DP:FA 0/1:102,11:32.0:113:0.097 0:159,0:.:160:0.0 -12 46287550 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:96,11:29.0:107:0.103:2 0:163,0:.:163:0.0:0 -12 49428717 rs148688181 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:536,45:30.0:581:0.077:2 0:436,1:.:437:0.002288:0 -12 49431654 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:584,110:30.0:694:0.159:2 0:493,0:.:495:0.0:0 -12 49436248 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:250,45:29.0:295:0.153:2 0:208,0:.:208:0.0:0 -12 49438490 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:334,145:30.0:479:0.303:2 0:406,0:.:406:0.0:0 -12 50413034 rs76465602 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:133,8:32.0:141:0.057:2 0:142,1:.:143:0.006993:0 -12 50484405 rs79510657 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:224,59:31.0:283:0.208:2 0:258,0:.:259:0.0:0 -12 52906545 rs79750494 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:57,4:30.0:62:0.066:2 0:49,0:.:49:0.0:0 -12 52921297 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:279,24:30.0:303:0.079:2 0:180,0:.:180:0.0:0 -12 53030489 rs73109357 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:65,11:31.0:76:0.145:2 0:61,0:.:61:0.0:0 -12 55427158 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:95,7:31.0:102:0.069:2 0:56,0:.:56:0.0:0 -12 56489613 rs138072655 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:253,75:32.0:328:0.229:2 0:316,0:.:316:0.0:0 -12 57860293 rs182191937 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:146,10:32.0:156:0.064:2 0:94,0:.:94:0.0:0 -12 57865284 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1130,70:30.0:1201:0.058:2 0:1100,0:.:1101:0.0:0 -12 58144359 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:146,78:29.0:224:0.348:2 0:160,0:.:161:0.0:0 -12 61873046 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:225,11:31.0:236:0.047:2 0:224,0:.:224:0.0:0 -12 69202867 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:120,13:30.0:133:0.098:2 0:74,0:.:74:0.0:0 -12 77054235 rs12817158 G T . PASS DB GT:AD:BQ:DP:FA 0/1:40,53:30.0:93:0.57 0:80,3:.:83:0.036 -12 87756834 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:3,3:31.0:6:0.5:2 0:11,0:.:11:0.0:0 -12 91238015 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:46,15:30.0:61:0.246:2 0:67,0:.:67:0.0:0 -12 97487834 . T G . PASS . GT:AD:BQ:DP:FA 0/1:301,8:29.0:309:0.026 0:344,1:.:345:0.002899 -12 115109672 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:564,28:28.0:592:0.047:2 0:601,1:.:602:0.001661:0 -12 115110078 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:295,11:30.0:306:0.036:2 0:253,0:.:253:0.0:0 -12 115112315 . G T . PASS . GT:AD:BQ:DP:FA 0/1:75,14:31.0:89:0.157 0:70,2:.:72:0.028 -12 115117337 rs34627348 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:543,113:30.0:656:0.172:2 0:733,0:.:733:0.0:0 -12 115118589 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:163,29:31.0:192:0.151:2 0:172,0:.:172:0.0:0 -12 120541570 rs17499109 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:510,154:29.0:664:0.232:2 0:441,1:.:442:0.002262:0 -12 120541597 rs73217390 G A . PASS DB GT:AD:BQ:DP:FA 0/1:710,206:29.0:917:0.225 0:671,2:.:673:0.002972 -12 120554466 rs191322615 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:238,183:30.0:421:0.435:2 0:319,1:.:321:0.003125:0 -12 121435778 rs56097722 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:53,7:27.0:60:0.117:2 0:41,0:.:41:0.0:0 -12 132001302 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:5,3:29.0:8:0.375:2 0:10,0:.:10:0.0:0 -12 132001303 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:5,3:27.0:8:0.375:2 0:10,0:.:10:0.0:0 -12 133208752 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:41,5:30.0:46:0.109:2 0:32,0:.:32:0.0:0 -12 133211059 rs5745004 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:61,31:31.0:92:0.337:2 0:70,0:.:70:0.0:0 -12 133257837 rs34047482 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:345,21:30.0:368:0.057:2 0:436,1:.:438:0.002288:0 -13 21004758 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:216,11:31.0:227:0.048:2 0:239,0:.:239:0.0:0 -13 28611186 rs17086239 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:25,20:31.0:45:0.444:2 0:47,1:.:48:0.021:0 -13 28611221 rs17086242 T C . PASS DB GT:AD:BQ:DP:FA 0/1:45,31:31.0:76:0.408 0:82,3:.:86:0.035 -13 28644610 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:275,27:33.0:302:0.089:2 0:348,0:.:348:0.0:0 -13 28964198 rs17537350 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:365,13:31.0:378:0.034:2 0:402,1:.:403:0.002481:0 -13 28971220 . G A . PASS . GT:AD:BQ:DP:FA 0/1:165,64:30.0:229:0.279 0:220,2:.:223:0.009009 -13 32747212 rs17077178 C G . PASS DB GT:AD:BQ:DP:FA 0/1:59,45:31.0:104:0.433 0:116,4:.:120:0.033 -13 32899388 rs11571610 A C . PASS DB GT:AD:BQ:DP:FA 0/1:51,46:30.0:97:0.474 0:140,8:.:148:0.054 -13 32906480 rs766173 A C . PASS DB GT:AD:BQ:DP:FA 0/1:297,202:32.0:499:0.405 0:476,27:.:504:0.054 -13 32906980 rs1801439 A G . PASS DB GT:AD:BQ:DP:FA 0/1:153,98:30.0:251:0.39 0:247,15:.:262:0.057 -13 32910351 rs11571651 G T . PASS DB GT:AD:BQ:DP:FA 0/1:178,156:30.0:334:0.467 0:330,27:.:357:0.076 -13 32910721 rs1801499 T C . PASS DB GT:AD:BQ:DP:FA 0/1:683,489:32.0:1173:0.417 0:1172,90:.:1263:0.071 -13 32911463 rs1799944 A G . PASS DB GT:AD:BQ:DP:FA 0/1:630,521:31.0:1151:0.453 0:1174,81:.:1255:0.065 -13 32929478 rs11147489 C T . PASS DB GT:AD:BQ:DP:FA 0/1:422,423:31.0:847:0.501 0:910,63:.:976:0.065 -13 32930673 rs28897744 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:317,104:30.0:421:0.247:2 0:473,1:.:474:0.00211:0 -13 32968793 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:144,14:33.0:158:0.089:2 0:171,0:.:171:0.0:0 -13 41032432 rs17258297 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:85,44:31.0:130:0.341:2 0:130,0:.:131:0.0:0 -13 41161979 rs2984121 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:722,51:32.0:773:0.066:2 0:790,0:.:790:0.0:0 -13 49037825 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:218,27:30.0:245:0.11:2 0:232,1:.:233:0.004292:0 -13 49047529 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:172,113:32.0:286:0.396:2 0:338,0:.:339:0.0:0 -13 67591561 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:70,31:31.0:101:0.307:2 0:64,0:.:64:0.0:0 -13 67591562 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:73,30:32.0:103:0.291:2 0:65,0:.:65:0.0:0 -13 68406205 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:44,10:27.0:54:0.185:2 0:52,0:.:52:0.0:0 -13 73348372 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:16,3:33.0:19:0.158:2 0:11,0:.:11:0.0:0 -13 103504331 rs41548912 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:47,4:30.0:51:0.078:2 0:34,0:.:34:0.0:0 -13 103508378 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:189,36:30.0:225:0.16:2 0:235,1:.:236:0.004237:0 -13 106826430 rs1887896 G T . PASS DB GT:AD:BQ:DP:FA 0/1:154,48:30.0:202:0.238 0:222,6:.:228:0.026 -13 110428923 rs9559654 G A . PASS DB GT:AD:BQ:DP:FA 0/1:50,159:28.0:209:0.761 0:155,7:.:162:0.043 -13 110435914 rs12853546 G A . PASS DB GT:AD:BQ:DP:FA 0/1:43,136:30.0:179:0.76 0:130,3:.:133:0.023 -14 20893115 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:275,19:31.0:294:0.065:2 0:154,0:.:154:0.0:0 -14 23652305 rs73600433 A C . PASS DB GT:AD:BQ:DP:FA 0/1:621,390:31.0:1011:0.386 0:804,37:.:841:0.044 -14 23764770 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:68,20:32.0:88:0.227:2 0:48,0:.:48:0.0:0 -14 25438196 rs78425257 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:318,29:31.0:347:0.084:2 0:180,0:.:180:0.0:0 -14 35872920 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:3872,168:30.0:4042:0.042:2 0:1249,0:.:1249:0.0:0 -14 36988175 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:218,1008:30.0:1227:0.822:2 0:150,0:.:150:0.0:0 -14 38060768 rs35342092 G A . PASS DB GT:AD:BQ:DP:FA 0/1:5080,126:31.0:5207:0.024 0:1372,3:.:1377:0.002182 -14 38061106 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:626,24:30.0:651:0.037:2 0:128,0:.:128:0.0:0 -14 48351664 rs61993497 A G . PASS DB GT:AD:BQ:DP:FA 0/1:202,33:33.0:235:0.14 0:177,5:.:182:0.027 -14 61799788 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:287,42:31.0:329:0.128:2 0:248,0:.:248:0.0:0 -14 65544815 rs184998980 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:125,67:29.0:192:0.349:2 0:103,0:.:103:0.0:0 -14 65568285 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:291,20:31.0:311:0.064:2 0:297,0:.:299:0.0:0 -14 69061259 rs28908468 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:151,76:31.0:227:0.335:2 0:141,0:.:141:0.0:0 -14 69117298 rs79769103 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:48,7:30.0:55:0.127:2 0:28,0:.:28:0.0:0 -14 69117450 rs74506607 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:490,67:32.0:557:0.12:2 0:385,0:.:385:0.0:0 -14 70439711 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:13,3:31.0:16:0.188:2 0:8,0:.:8:0.0:0 -14 77493815 rs7156498 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:26,3:32.0:29:0.103:2 0:54,0:.:54:0.0:0 -14 80471852 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:255,43:31.0:298:0.144:2 0:221,0:.:221:0.0:0 -14 81563195 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:83,20:31.0:103:0.194:2 0:25,0:.:25:0.0:0 -14 87813148 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:111,6:32.0:117:0.051:2 0:69,0:.:69:0.0:0 -14 87813214 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:37,7:31.0:44:0.159:2 0:20,0:.:20:0.0:0 -14 88360375 rs35362358 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:13,10:30.0:23:0.435:2 0:20,0:.:20:0.0:0 -14 95556644 . A C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:22,6:32.0:28:0.214:2 0:11,0:.:11:0.0:0 -14 95560444 rs139500905 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:345,24:29.0:369:0.065:2 0:278,0:.:278:0.0:0 -14 95562999 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:693,60:29.0:754:0.08:2 0:532,0:.:533:0.0:0 -14 95591070 rs67737119 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:47,32:31.0:79:0.405:2 0:45,0:.:45:0.0:0 -14 103707780 rs17101400 G A . PASS DB GT:AD:BQ:DP:FA 0/1:25,9:31.0:34:0.265 0:30,1:.:31:0.032 -14 105238820 rs61761201 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:451,37:32.0:489:0.076:2 0:254,0:.:255:0.0:0 -14 105241103 . C G . PASS . GT:AD:BQ:DP:FA 0/1:69,4:31.0:73:0.055 0:16,0:.:16:0.0 -14 105241378 rs3730346 C T . PASS DB GT:AD:BQ:DP:FA 0/1:870,305:31.0:1176:0.26 0:548,13:.:565:0.023 -14 105241607 rs182149357 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:292,109:31.0:401:0.272:2 0:183,0:.:184:0.0:0 -15 26216159 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:21,3:32.0:24:0.125:2 0:10,0:.:10:0.0:0 -15 35385071 rs28629832 C T . PASS DB GT:AD:BQ:DP:FA 0/1:322,218:31.0:542:0.404 0:538,26:.:565:0.046 -15 42046575 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:240,10:30.0:250:0.04:2 0:199,0:.:199:0.0:0 -15 59845326 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:7,4:29.0:11:0.364:2 0:11,0:.:11:0.0:0 -15 64281668 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:7,4:32.0:11:0.364:2 0:12,0:.:12:0.0:0 -15 66679684 rs77796976 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:653,52:32.0:705:0.074:2 0:766,0:.:766:0.0:0 -15 66779698 rs41315964 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:156,43:30.0:200:0.216:2 0:204,0:.:205:0.0:0 -15 66782048 rs41306345 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:387,81:30.0:468:0.173:2 0:554,0:.:554:0.0:0 -15 67473790 rs117185005 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:260,181:30.0:441:0.41:2 0:397,0:.:400:0.0:0 -15 88126117 rs118139016 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:143,94:29.0:238:0.397:2 0:262,1:.:264:0.003802:0 -15 88472228 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:35,6:31.0:41:0.146:2 0:17,0:.:17:0.0:0 -15 88472655 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:240,161:30.0:401:0.401:2 0:286,0:.:287:0.0:0 -15 91292969 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:372,19:30.0:391:0.049:2 0:401,0:.:402:0.0:0 -15 92829452 rs28566962 G A . PASS DB GT:AD:BQ:DP:FA 0/1:96,77:30.0:173:0.445 0:124,8:.:132:0.061 -15 99460184 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:112,34:30.0:146:0.233:2 0:117,0:.:117:0.0:0 -15 99467930 rs186895929 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:322,78:30.0:401:0.195:2 0:317,1:.:318:0.003145:0 -15 99861641 rs149886786 T G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:250,52:31.0:302:0.172:2 0:315,0:.:315:0.0:0 -16 339415 rs387467 G T . PASS DB GT:AD:BQ:DP:FA 0/1:360,168:30.0:531:0.318 0:323,16:.:339:0.047 -16 339727 rs423749 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:63,29:27.0:92:0.315:2 0:43,0:.:43:0.0:0 -16 347184 rs214252 A G . PASS DB GT:AD:BQ:DP:FA 0/1:517,191:30.0:708:0.27 0:549,16:.:567:0.028 -16 347326 rs214251 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:72,36:30.0:108:0.333:2 0:43,0:.:43:0.0:0 -16 360149 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:195,9:30.0:204:0.044:2 0:118,0:.:118:0.0:0 -16 396234 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:595,22:30.0:617:0.036:2 0:513,0:.:513:0.0:0 -16 1987179 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:31,7:30.0:38:0.184:2 0:30,0:.:30:0.0:0 -16 2110795 rs1800725 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:510,125:31.0:635:0.197:2 0:471,1:.:472:0.002119:0 -16 2132583 rs1800705 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:140,81:30.0:222:0.367:2 0:126,0:.:127:0.0:0 -16 2134852 rs148656621 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:217,109:30.0:326:0.334:2 0:156,0:.:157:0.0:0 -16 2136455 rs76029733 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:173,36:29.0:209:0.172:2 0:107,0:.:107:0.0:0 -16 2215659 . C G . PASS . GT:AD:BQ:DP:FA 0/1:58,8:27.0:66:0.121 0:18,0:.:18:0.0 -16 2215660 . T C . PASS . GT:AD:BQ:DP:FA 0/1:57,10:30.0:67:0.149 0:20,0:.:20:0.0 -16 2226763 rs184220090 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:58,7:32.0:65:0.108:2 0:21,0:.:21:0.0:0 -16 3786594 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:351,44:31.0:396:0.111:2 0:305,0:.:305:0.0:0 -16 3794705 rs129972 T G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:53,14:30.0:67:0.209:2 0:41,0:.:41:0.0:0 -16 3807171 rs140586932 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:28,16:30.0:44:0.364:2 0:58,0:.:59:0.0:0 -16 3807946 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:402,33:30.0:435:0.076:2 0:472,0:.:472:0.0:0 -16 3860554 rs190677981 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:201,103:31.0:304:0.339:2 0:243,0:.:243:0.0:0 -16 10273821 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:269,18:31.0:287:0.063:2 0:208,0:.:208:0.0:0 -16 10353357 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:9,3:31.0:12:0.25:2 0:13,0:.:13:0.0:0 -16 14028861 rs3136150 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:32,7:31.0:39:0.179:2 0:28,0:.:28:0.0:0 -16 14041760 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:513,16:29.0:529:0.03:2 0:568,0:.:568:0.0:0 -16 14042077 rs1800124 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:439,45:32.0:484:0.093:2 0:502,0:.:502:0.0:0 -16 27356584 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:83,47:32.0:130:0.362:2 0:108,0:.:108:0.0:0 -16 30129936 rs12922100 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:152,86:30.0:238:0.361:2 0:197,1:.:198:0.005051:0 -16 33373312 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:463,22:29.0:485:0.045:2 0:911,0:.:911:0.0:0 -16 56866196 rs2241770 T C . PASS DB GT:AD:BQ:DP:FA 0/1:658,159:31.0:817:0.195 0:812,27:.:840:0.032 -16 56871762 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:72,15:32.0:87:0.172:2 0:56,0:.:56:0.0:0 -16 56872824 rs3764266 G A . PASS DB GT:AD:BQ:DP:FA 0/1:432,128:29.0:560:0.229 0:541,25:.:566:0.044 -16 58960831 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:40,24:29.0:64:0.375:2 0:44,0:.:44:0.0:0 -16 68862182 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:343,13:32.0:357:0.037:2 0:423,0:.:423:0.0:0 -16 72822296 rs2228199 G A . PASS DB GT:AD:BQ:DP:FA 0/1:1075,240:31.0:1317:0.183 0:1381,51:.:1433:0.036 -16 72828383 . C T . PASS . GT:AD:BQ:DP:FA 0/1:820,207:30.0:1029:0.202 0:1009,3:.:1013:0.002964 -16 72830539 rs62051555 C G . PASS DB GT:AD:BQ:DP:FA 0/1:1106,215:32.0:1323:0.163 0:1311,41:.:1355:0.03 -16 72832377 . G A . PASS . GT:AD:BQ:DP:FA 0/1:1072,49:31.0:1121:0.044 0:1065,3:.:1070:0.002809 -16 72991718 . G A . PASS . GT:AD:BQ:DP:FA 0/1:681,7:29.0:688:0.01 0:590,1:.:592:0.001692 -16 72993622 rs62053190 C T . PASS DB GT:AD:BQ:DP:FA 0/1:805,143:31.0:949:0.151 0:964,27:.:996:0.027 -16 72993706 rs62053191 G A . PASS DB GT:AD:BQ:DP:FA 0/1:834,150:30.0:984:0.152 0:981,25:.:1006:0.025 -16 81887977 rs34028338 G C . PASS DB GT:AD:BQ:DP:FA 0/1:149,82:31.0:231:0.355 0:207,7:.:214:0.033 -16 81888274 rs41305759 C A . PASS DB GT:AD:BQ:DP:FA 0/1:143,97:30.0:240:0.404 0:223,11:.:234:0.047 -16 81891790 rs36114479 C G . PASS DB GT:AD:BQ:DP:FA 0/1:186,82:32.0:268:0.306 0:230,7:.:237:0.03 -16 81892645 rs150054348 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:111,25:31.0:136:0.184:2 0:123,0:.:123:0.0:0 -16 81892646 rs185238046 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:119,22:30.0:141:0.156:2 0:131,0:.:131:0.0:0 -16 81892913 rs12596639 C T . PASS DB GT:AD:BQ:DP:FA 0/1:91,37:31.0:128:0.289 0:98,4:.:102:0.039 -16 81917099 rs6564928 G T . PASS DB GT:AD:BQ:DP:FA 0/1:66,26:30.0:92:0.283 0:65,3:.:68:0.044 -16 81946328 rs138158454 G A . PASS DB GT:AD:BQ:DP:FA 0/1:603,316:29.0:920:0.344 0:803,3:.:807:0.003722 -16 81957227 rs4485361 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:469,101:30.0:570:0.177:2 0:552,0:.:552:0.0:0 -16 81957349 rs117954043 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:85,13:29.0:98:0.133:2 0:43,0:.:43:0.0:0 -16 81990505 rs45491692 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:465,238:30.0:705:0.339:2 0:701,0:.:704:0.0:0 -16 89350597 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1331,164:32.0:1496:0.11:2 0:1549,0:.:1550:0.0:0 -16 89357823 . C G . PASS . GT:AD:BQ:DP:FA 0/1:39,3:30.0:42:0.071 0:9,0:.:9:0.0 -16 89839915 rs117477270 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:72,6:31.0:79:0.077:2 0:65,0:.:65:0.0:0 -17 3568401 rs3817666 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:16,8:30.0:24:0.333:2 0:22,0:.:22:0.0:0 -17 4540268 rs11568145 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:127,11:32.0:139:0.08:2 0:147,0:.:147:0.0:0 -17 7577407 rs12951053 A C . PASS DB GT:AD:BQ:DP:FA 0/1:49,67:32.0:116:0.578 0:139,6:.:146:0.041 -17 7577427 rs12947788 G A . PASS DB GT:AD:BQ:DP:FA 0/1:59,84:30.0:143:0.587 0:184,8:.:195:0.042 -17 7578461 rs121912654 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:206,108:30.0:314:0.344:2 0:436,0:.:438:0.0:0 -17 7580500 rs12944939 C T . PASS DB GT:AD:BQ:DP:FA 0/1:30,65:31.0:95:0.684 0:95,3:.:98:0.031 -17 7976917 rs78835850 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:161,69:29.0:230:0.3:2 0:208,0:.:209:0.0:0 -17 7983681 rs2304906 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:269,32:30.0:301:0.106:2 0:273,0:.:273:0.0:0 -17 7984157 rs3816263 A C . PASS DB GT:AD:BQ:DP:FA 0/1:398,119:31.0:517:0.23 0:423,16:.:439:0.036 -17 15983458 rs118072442 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:118,75:30.0:193:0.389:2 0:176,0:.:176:0.0:0 -17 16049563 rs183071464 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:88,11:30.0:99:0.111:2 0:87,1:.:88:0.011:0 -17 21544599 rs9912297 A G . PASS DB GT:AD:BQ:DP:FA 0/1:251,121:31.0:372:0.325 0:318,14:.:332:0.042 -17 29585907 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:38,8:30.0:46:0.174:2 0:13,0:.:13:0.0:0 -17 29587341 rs17881285 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:264,51:30.0:315:0.162:2 0:306,0:.:306:0.0:0 -17 30315470 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:556,129:30.0:686:0.188:2 0:747,0:.:748:0.0:0 -17 33430327 . C A . PASS . GT:AD:BQ:DP:FA 0/1:666,69:30.0:736:0.094 0:689,3:.:693:0.004335 -17 37618220 rs192819848 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:87,14:31.0:101:0.139:2 0:57,0:.:57:0.0:0 -17 37646947 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:621,25:29.0:646:0.039:2 0:595,0:.:595:0.0:0 -17 37866797 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:171,31:27.0:204:0.153:2 0:128,0:.:128:0.0:0 -17 37871848 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:307,44:30.0:351:0.125:2 0:201,0:.:201:0.0:0 -17 38497450 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:78,9:30.0:87:0.103:2 0:20,0:.:20:0.0:0 -17 38497833 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:443,22:30.0:465:0.047:2 0:384,1:.:385:0.002597:0 -17 38497884 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:393,67:30.0:461:0.146:2 0:407,1:.:408:0.002451:0 -17 38512197 rs8069541 T C . PASS DB GT:AD:BQ:DP:FA 0/1:172,124:31.0:296:0.419 0:168,11:.:179:0.061 -17 38512457 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:787,30:31.0:818:0.037:2 0:572,0:.:574:0.0:0 -17 38512461 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:779,30:30.0:811:0.037:2 0:575,1:.:579:0.001736:0 -17 40467934 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:349,12:30.0:361:0.033:2 0:205,0:.:205:0.0:0 -17 40489660 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:617,32:30.0:651:0.049:2 0:546,0:.:548:0.0:0 -17 41244880 rs80357200 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:441,45:31.0:487:0.093:2 0:384,0:.:385:0.0:0 -17 41267608 . G C . PASS . GT:AD:BQ:DP:FA 0/1:153,6:32.0:160:0.038 0:121,0:.:121:0.0 -17 43344458 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:436,21:30.0:457:0.046:2 0:364,0:.:364:0.0:0 -17 43352049 rs17685379 C T . PASS DB GT:AD:BQ:DP:FA 0/1:29,256:28.0:285:0.898 0:111,9:.:120:0.075 -17 46801231 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:193,10:29.0:203:0.049:2 0:107,0:.:107:0.0:0 -17 46802314 rs116931900 G T . PASS DB GT:AD:BQ:DP:FA 0/1:52,4:30.0:56:0.071 0:27,0:.:27:0.0 -17 54445637 rs71137202 C G . PASS DB GT:AD:BQ:DP:FA 0/1:79,13:31.0:92:0.141 0:86,0:.:90:0.0 -17 56440474 rs2632517 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:132,26:30.0:158:0.165:2 0:60,0:.:60:0.0:0 -17 56440642 rs76384648 C T . PASS DB GT:AD:BQ:DP:FA 0/1:1157,52:30.0:1209:0.043 0:823,0:.:825:0.0 -17 56811731 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:44,4:31.0:48:0.083:2 0:29,0:.:29:0.0:0 -17 58678009 . T A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:517,105:31.0:624:0.169:2 0:538,1:.:540:0.001855:0 -17 59924512 rs4988346 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:863,40:29.0:905:0.044:2 0:720,0:.:720:0.0:0 -17 59926645 rs4988343 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:160,114:28.0:274:0.416:2 0:163,0:.:163:0.0:0 -17 61307713 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:12,3:33.0:15:0.2:2 0:10,0:.:10:0.0:0 -17 62008760 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:491,216:30.0:708:0.306:2 0:474,0:.:474:0.0:0 -17 70120111 rs929651 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:173,18:31.0:191:0.094:2 0:66,0:.:66:0.0:0 -17 77280452 rs117415787 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:24,36:32.0:60:0.6:2 0:26,0:.:26:0.0:0 -17 78796907 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:500,27:32.0:530:0.051:2 0:422,0:.:423:0.0:0 -17 78829114 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:87,5:33.0:92:0.054:2 0:52,0:.:52:0.0:0 -17 78857631 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:612,33:30.0:645:0.051:2 0:437,0:.:437:0.0:0 -17 78919466 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:783,27:31.0:810:0.033:2 0:617,0:.:618:0.0:0 -17 78934088 rs77734083 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:91,66:32.0:157:0.42:2 0:86,0:.:86:0.0:0 -18 8413657 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:476,30:30.0:506:0.059:2 0:376,0:.:376:0.0:0 -18 12912750 rs74405000 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:95,7:30.0:102:0.069:2 0:81,0:.:81:0.0:0 -18 12912821 rs74870438 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:329,19:31.0:348:0.055:2 0:314,0:.:314:0.0:0 -18 18517151 . A C . PASS . GT:AD:BQ:DP:FA 0/1:4,3:31.0:7:0.429 0:47,5:.:52:0.096 -18 28787634 rs78796387 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:40,9:30.0:49:0.184:2 0:51,1:.:52:0.019:0 -18 39537688 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:212,166:32.0:378:0.439:2 0:434,0:.:434:0.0:0 -18 48190817 rs45471400 G A . PASS DB GT:AD:BQ:DP:FA 0/1:68,64:29.0:132:0.485 0:148,12:.:160:0.075 -19 1221161 rs9282860 C T . PASS DB GT:AD:BQ:DP:FA 0/1:301,156:30.0:457:0.341 0:398,20:.:418:0.048 -19 1611856 rs62130064 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:674,37:30.0:711:0.052:2 0:744,1:.:745:0.001342:0 -19 1622115 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:813,25:31.0:838:0.03:2 0:649,0:.:651:0.0:0 -19 2211220 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:405,17:31.0:424:0.04:2 0:382,0:.:382:0.0:0 -19 2217203 rs72985483 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:52,7:30.0:59:0.119:2 0:33,0:.:33:0.0:0 -19 3110361 rs41276846 C T . PASS DB GT:AD:BQ:DP:FA 0/1:171,72:30.0:243:0.296 0:242,8:.:251:0.032 -19 3114864 rs3746069 C T . PASS DB GT:AD:BQ:DP:FA 0/1:120,42:31.0:163:0.259 0:119,5:.:124:0.04 -19 3118851 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:214,18:29.0:232:0.078:2 0:129,0:.:129:0.0:0 -19 4102449 rs17851657 G A . PASS DB GT:AD:BQ:DP:FA 0/1:166,280:31.0:446:0.628 0:427,31:.:458:0.068 -19 5174304 rs76272020 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:22,9:28.0:31:0.29:2 0:20,0:.:20:0.0:0 -19 5206724 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:186,84:30.0:270:0.311:2 0:240,0:.:240:0.0:0 -19 5208216 rs60630722 G A . PASS DB GT:AD:BQ:DP:FA 0/1:187,198:30.0:385:0.514 0:313,24:.:337:0.071 -19 5208257 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:555,37:30.0:592:0.063:2 0:556,0:.:556:0.0:0 -19 5212482 rs2230611 G A . PASS DB GT:AD:BQ:DP:FA 0/1:216,302:30.0:518:0.583 0:490,21:.:511:0.041 -19 5212586 rs4807696 G T . PASS DB GT:AD:BQ:DP:FA 0/1:73,82:30.0:155:0.529 0:105,6:.:111:0.054 -19 5218684 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:189,80:31.0:269:0.297:2 0:170,0:.:170:0.0:0 -19 5222088 rs3746131 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:107,113:32.0:220:0.514:2 0:188,0:.:188:0.0:0 -19 5229728 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:10,5:30.0:15:0.333:2 0:15,0:.:15:0.0:0 -19 5240392 rs3746130 C T . PASS DB GT:AD:BQ:DP:FA 0/1:139,95:29.0:234:0.406 0:193,8:.:201:0.04 -19 7123031 rs148813626 G A . PASS DB GT:AD:BQ:DP:FA 0/1:247,146:30.0:395:0.372 0:358,14:.:372:0.038 -19 7132343 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:133,67:31.0:200:0.335:2 0:198,0:.:198:0.0:0 -19 7162968 . C T . PASS . GT:AD:BQ:DP:FA 0/1:149,5:32.0:154:0.032 0:160,0:.:160:0.0 -19 7172526 rs41412545 C A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:40,26:31.0:66:0.394:2 0:66,0:.:66:0.0:0 -19 7184238 rs6510959 G A . PASS DB GT:AD:BQ:DP:FA 0/1:71,76:28.0:147:0.517 0:148,11:.:160:0.069 -19 7184243 rs41315074 C G . PASS DB GT:AD:BQ:DP:FA 0/1:80,79:32.0:159:0.497 0:173,8:.:181:0.044 -19 7184490 . G A . PASS . GT:AD:BQ:DP:FA 0/1:240,133:31.0:374:0.357 0:471,2:.:473:0.004228 -19 7805951 rs11465413 A T . PASS DB GT:AD:BQ:DP:FA 0/1:45,711:31.0:756:0.94 0:780,53:.:833:0.064 -19 7815690 rs111296792 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:36,13:31.0:49:0.265:2 0:45,0:.:45:0.0:0 -19 10260400 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:142,7:30.0:149:0.047:2 0:137,0:.:137:0.0:0 -19 10278953 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:284,74:32.0:358:0.207:2 0:407,0:.:408:0.0:0 -19 10292608 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:71,7:27.0:78:0.09:2 0:82,0:.:82:0.0:0 -19 10292901 rs78789647 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:33,7:30.0:40:0.175:2 0:33,1:.:34:0.029:0 -19 10610017 rs12985702 G C . PASS DB GT:AD:BQ:DP:FA 0/1:131,94:30.0:225:0.418 0:228,10:.:238:0.042 -19 11130431 rs45565139 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:231,92:31.0:323:0.285:2 0:361,1:.:362:0.002762:0 -19 11169305 rs36049922 T C . PASS DB GT:AD:BQ:DP:FA 0/1:47,28:32.0:75:0.373 0:39,2:.:42:0.049 -19 13051554 rs184881678 G T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:695,319:30.0:1014:0.315:2 0:979,0:.:984:0.0:0 -19 14627140 rs45454593 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:792,338:30.0:1132:0.299:2 0:1274,1:.:1276:0.0007843:0 -19 14629336 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:23,11:31.0:34:0.324:2 0:20,0:.:20:0.0:0 -19 15291576 rs35769976 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:423,210:32.0:633:0.332:2 0:532,0:.:534:0.0:0 -19 15291699 rs57538005 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:233,97:31.0:330:0.294:2 0:220,0:.:222:0.0:0 -19 15296513 rs147014533 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:276,115:28.0:392:0.294:2 0:320,0:.:321:0.0:0 -19 15299048 rs114207045 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:392,188:30.0:580:0.324:2 0:494,0:.:494:0.0:0 -19 15308287 rs188132716 G C . PASS DB GT:AD:BQ:DP:FA 0/1:390,171:30.0:561:0.305 0:487,2:.:489:0.00409 -19 15890626 rs55782900 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:37,58:31.0:95:0.611:2 0:73,1:.:74:0.014:0 -19 17953950 rs55778349 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:395,27:30.0:422:0.064:2 0:407,1:.:409:0.002451:0 -19 18271576 rs11670635 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:49,17:30.0:66:0.258:2 0:44,0:.:44:0.0:0 -19 18277820 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:90,11:32.0:101:0.109:2 0:73,0:.:73:0.0:0 -19 18279861 . C T . PASS . GT:AD:BQ:DP:FA 0/1:268,6:31.0:275:0.022 0:219,0:.:219:0.0 -19 18280096 rs149081991 G A . PASS DB GT:AD:BQ:DP:FA 0/1:37,19:29.0:56:0.339 0:58,2:.:60:0.033 -19 19260105 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:494,21:31.0:515:0.041:2 0:444,0:.:444:0.0:0 -19 30311555 rs201798088 C T . PASS DB GT:AD:BQ:DP:FA 0/1:193,14:29.0:207:0.068 0:130,2:.:132:0.015 -19 30312874 rs3218066 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:381,238:30.0:619:0.384:2 0:475,0:.:475:0.0:0 -19 30313622 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:78,9:29.0:87:0.103:2 0:60,0:.:60:0.0:0 -19 33905969 rs77619050 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:25,9:30.0:34:0.265:2 0:19,0:.:19:0.0:0 -19 34080443 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:52,32:31.0:84:0.381:2 0:54,0:.:54:0.0:0 -19 34080444 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:52,32:30.0:84:0.381:2 0:53,0:.:53:0.0:0 -19 39538680 rs116959993 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:95,17:30.0:112:0.152:2 0:82,0:.:82:0.0:0 -19 41727143 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:512,117:31.0:629:0.186:2 0:501,0:.:506:0.0:0 -19 41727197 rs2271546 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:255,76:30.0:331:0.23:2 0:221,0:.:221:0.0:0 -19 41749397 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:221,17:30.0:238:0.071:2 0:142,0:.:142:0.0:0 -19 41759474 rs73045223 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:480,41:30.0:521:0.079:2 0:375,0:.:375:0.0:0 -19 41763269 rs141726434 A T . PASS DB GT:AD:BQ:DP:FA 0/1:152,5:31.0:157:0.032 0:100,0:.:100:0.0 -19 42384572 rs141689896 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:131,8:29.0:139:0.058:2 0:64,1:.:65:0.015:0 -19 42790821 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:310,13:31.0:324:0.04:2 0:215,1:.:217:0.00463:0 -19 42791015 . C A . PASS . GT:AD:BQ:DP:FA 0/1:822,41:30.0:863:0.048 0:560,2:.:563:0.003559 -19 42795554 rs10410185 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:832,146:30.0:979:0.149:2 0:710,1:.:713:0.001406:0 -19 42797603 rs78756053 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:92,15:31.0:107:0.14:2 0:30,0:.:30:0.0:0 -19 45856260 rs185386615 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:289,21:30.0:310:0.068:2 0:209,0:.:209:0.0:0 -19 50906507 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:499,53:30.0:552:0.096:2 0:476,1:.:478:0.002096:0 -19 50910196 rs3219396 A G . PASS DB GT:AD:BQ:DP:FA 0/1:537,65:28.0:604:0.108 0:568,2:.:576:0.003509 -19 50912821 rs144143245 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:773,98:31.0:871:0.113:2 0:762,0:.:766:0.0:0 -19 50916796 . G A . PASS . GT:AD:BQ:DP:FA 0/1:565,6:30.0:571:0.011 0:535,1:.:536:0.001866 -19 52693297 rs111861947 C T . PASS DB GT:AD:BQ:DP:FA 0/1:150,6:30.0:156:0.038 0:136,0:.:136:0.0 -20 1421974 rs35310517 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:140,26:33.0:166:0.157:2 0:110,0:.:110:0.0:0 -20 30296422 rs73117925 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:196,100:31.0:297:0.338:2 0:206,0:.:206:0.0:0 -20 30296428 rs117532975 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:263,68:30.0:331:0.205:2 0:216,0:.:216:0.0:0 -20 30296664 . G C . PASS . GT:AD:BQ:DP:FA 0/1:203,7:29.0:210:0.033 0:112,0:.:112:0.0 -20 30309960 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:497,24:33.0:521:0.046:2 0:387,0:.:387:0.0:0 -20 31016119 rs6087903 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1069,153:30.0:1222:0.125:2 0:924,1:.:925:0.001081:0 -20 31019299 . C T . PASS . GT:AD:BQ:DP:FA 0/1:676,66:29.0:742:0.089 0:494,2:.:497:0.004032 -20 39704995 rs6072262 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:137,26:30.0:163:0.16:2 0:136,0:.:136:0.0:0 -20 39743905 rs6072275 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:156,22:30.0:178:0.124:2 0:79,0:.:79:0.0:0 -20 39751809 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:689,36:31.0:725:0.05:2 0:459,0:.:459:0.0:0 -20 40709305 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:40,5:29.0:45:0.111:2 0:12,0:.:12:0.0:0 -20 40714218 rs74355524 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:74,6:30.0:80:0.075:2 0:30,0:.:30:0.0:0 -20 40714305 rs143180826 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:270,58:31.0:328:0.177:2 0:159,0:.:159:0.0:0 -20 40714307 rs3092662 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:233,103:30.0:336:0.307:2 0:169,0:.:169:0.0:0 -20 40738926 rs148680893 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:311,44:30.0:355:0.124:2 0:190,0:.:190:0.0:0 -20 40746918 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:93,25:30.0:119:0.212:2 0:41,0:.:41:0.0:0 -20 40748532 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:423,21:30.0:444:0.047:2 0:270,0:.:270:0.0:0 -20 40748802 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:57,5:31.0:62:0.081:2 0:23,0:.:23:0.0:0 -20 40979469 rs187458546 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:81,20:30.0:101:0.198:2 0:56,0:.:56:0.0:0 -20 41101067 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:717,69:29.0:786:0.088:2 0:472,0:.:472:0.0:0 -20 46256424 rs6094752 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1101,357:30.0:1459:0.245:2 0:948,0:.:950:0.0:0 -20 46271008 rs147647230 G A . PASS DB GT:AD:BQ:DP:FA 0/1:1533,211:30.0:1745:0.121 0:1049,4:.:1055:0.003799 -20 46275917 rs149561356 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1648,117:30.0:1765:0.066:2 0:1063,0:.:1063:0.0:0 -20 46277834 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1141,84:31.0:1226:0.069:2 0:828,0:.:829:0.0:0 -20 46279842 . G A . PASS . GT:AD:BQ:DP:FA 0/1:820,13:30.0:833:0.016 0:596,4:.:600:0.006667 -20 54945145 rs34189236 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:340,97:30.0:437:0.222:2 0:212,0:.:212:0.0:0 -20 57428287 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:766,65:31.0:831:0.078:2 0:398,0:.:399:0.0:0 -21 11021107 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:1989,130:31.0:2119:0.061:2 0:2036,0:.:2036:0.0:0 -21 11021189 . G A . PASS . GT:AD:BQ:DP:FA 0/1:2000,67:29.0:2067:0.032 0:1911,6:.:1919:0.00313 -21 11029526 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:235,9:32.0:244:0.037:2 0:239,0:.:239:0.0:0 -21 11047650 . C T . PASS . GT:AD:BQ:DP:FA 0/1:934,9:28.0:943:0.009544 0:800,0:.:801:0.0 -21 11049346 . C T . PASS . GT:AD:BQ:DP:FA 0/1:181,10:30.0:191:0.052 0:177,3:.:180:0.017 -21 31384240 rs17793045 C T . PASS DB GT:AD:BQ:DP:FA 0/1:249,16:31.0:265:0.06 0:219,2:.:221:0.00905 -21 36164388 . G C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:23,9:31.0:33:0.281:2 0:21,0:.:21:0.0:0 -21 39795279 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:387,31:31.0:418:0.074:2 0:288,0:.:288:0.0:0 -21 42842591 rs61735794 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:705,24:31.0:731:0.033:2 0:587,1:.:588:0.001701:0 -21 42860532 rs117696554 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:126,8:30.0:134:0.06:2 0:71,0:.:72:0.0:0 -21 42866297 rs61735793 G A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:415,12:31.0:427:0.028:2 0:327,1:.:328:0.003049:0 -21 42867003 . A T . PASS . GT:AD:BQ:DP:FA 0/1:246,116:30.0:362:0.32 0:318,0:.:318:0.0 -21 42872398 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:745,76:31.0:821:0.093:2 0:650,0:.:651:0.0:0 -21 42878780 . T G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:463,42:31.0:506:0.083:2 0:372,0:.:372:0.0:0 -21 43124132 rs73906207 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:41,18:32.0:59:0.305:2 0:32,0:.:32:0.0:0 -21 43124281 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:31,6:33.0:37:0.162:2 0:14,0:.:15:0.0:0 -21 44524290 rs1065145 A C . PASS DB GT:AD:BQ:DP:FA 0/1:38,22:31.0:60:0.367 0:42,2:.:44:0.045 -21 45649498 rs61377223 C T . PASS DB GT:AD:BQ:DP:FA 0/1:204,6:29.0:210:0.029 0:166,1:.:167:0.005988 -21 45649748 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:541,71:30.0:613:0.116:2 0:551,0:.:551:0.0:0 -21 45651275 . G A . PASS . GT:AD:BQ:DP:FA 0/1:713,113:29.0:826:0.137 0:700,3:.:703:0.004267 -22 17519579 rs5748829 A G . PASS DB GT:AD:BQ:DP:FA 0/1:89,40:33.0:129:0.31 0:103,3:.:106:0.028 -22 24176232 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:278,22:31.0:300:0.073:2 0:189,0:.:189:0.0:0 -22 26388019 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:57,7:31.0:64:0.109:2 0:40,0:.:40:0.0:0 -22 29120915 rs17881298 T A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:202,27:30.0:229:0.118:2 0:202,1:.:203:0.004926:0 -22 29691910 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:292,47:31.0:340:0.139:2 0:269,0:.:270:0.0:0 -22 41525892 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:368,19:33.0:387:0.049:2 0:341,0:.:342:0.0:0 -22 41542838 rs9611506 T A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:236,26:30.0:262:0.099:2 0:273,0:.:273:0.0:0 -22 41562785 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:31,10:32.0:41:0.244:2 0:47,0:.:47:0.0:0 -22 41574383 rs1046088 A C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:673,67:31.0:740:0.091:2 0:720,0:.:720:0.0:0 -X 1314857 . G A . PASS . GT:AD:BQ:DP:FA 0/1:140,58:30.0:198:0.293 0:245,14:.:259:0.054 -X 1314858 . G T . PASS . GT:AD:BQ:DP:FA 0/1:141,60:31.0:201:0.299 0:246,15:.:261:0.057 -X 1325301 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:201,11:30.0:212:0.052:2 0:302,0:.:302:0.0:0 -X 1325426 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:224,106:31.0:330:0.321:2 0:469,0:.:469:0.0:0 -X 22516183 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:35,12:27.0:47:0.255:2 0:35,0:.:35:0.0:0 -X 39930099 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:141,9:30.0:150:0.06:2 0:119,0:.:119:0.0:0 -X 39933358 . G A . PASS . GT:AD:BQ:DP:FA 0/1:563,6:29.0:569:0.011 0:509,1:.:510:0.001961 -X 44896832 . C G . PASS . GT:AD:BQ:DP:FA 0/1:196,120:32.0:316:0.38 0:440,2:.:442:0.004525 -X 44896888 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:307,162:29.0:471:0.345:2 0:693,0:.:694:0.0:0 -X 47430627 . T G . PASS . GT:AD:BQ:DP:FA 0/1:144,6:31.0:150:0.04 0:161,1:.:162:0.006173 -X 53246599 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:34,13:32.0:47:0.277:2 0:41,0:.:41:0.0:0 -X 63415940 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:63,16:30.0:79:0.203:2 0:37,0:.:38:0.0:0 -X 63425821 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:127,42:30.0:170:0.249:2 0:143,0:.:145:0.0:0 -X 66766359 . C T . PASS . GT:AD:BQ:DP:FA 0/1:57,26:29.0:84:0.313 0:52,2:.:55:0.037 -X 66943769 . C A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:147,12:29.0:159:0.075:2 0:108,0:.:108:0.0:0 -X 70347614 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:70,15:30.0:85:0.176:2 0:63,0:.:63:0.0:0 -X 70352491 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:121,53:30.0:174:0.305:2 0:70,0:.:70:0.0:0 -X 70356829 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:597,93:32.0:690:0.135:2 0:608,0:.:609:0.0:0 -X 74803898 rs5937404 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:145,49:31.0:194:0.253:2 0:201,0:.:201:0.0:0 -X 76939830 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:484,42:33.0:526:0.08:2 0:634,0:.:634:0.0:0 -X 100057572 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:367,133:30.0:500:0.266:2 0:539,0:.:540:0.0:0 -X 100615505 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:220,39:31.0:259:0.151:2 0:239,0:.:239:0.0:0 -X 122035670 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:10,3:32.0:13:0.231:2 0:13,0:.:13:0.0:0 -X 123159533 rs79769028 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:58,8:32.0:66:0.121:2 0:29,0:.:29:0.0:0 -X 123183965 rs147386628 C G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:155,17:31.0:172:0.099:2 0:116,0:.:116:0.0:0 -X 123184027 rs7063522 C T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:386,39:31.0:425:0.092:2 0:355,0:.:356:0.0:0 -X 123184284 rs74386199 T A . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:74,10:31.0:84:0.119:2 0:49,0:.:49:0.0:0 -X 123191922 rs76876596 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:109,15:29.0:124:0.121:2 0:68,0:.:68:0.0:0 -X 123217527 rs75515623 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:75,12:32.0:87:0.138:2 0:31,0:.:31:0.0:0 -X 139479797 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:100,22:30.0:122:0.18:2 0:74,0:.:74:0.0:0 -Y 4971352 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:0,5:31.0:5:1.0:2 0:69,0:.:69:0.0:0 -MT 178 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:22,18:32.0:40:0.45:2 0:12,0:.:12:0.0:0 -MT 477 rs41442247 T C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:27,18:32.0:45:0.4:2 0:32,0:.:32:0.0:0 -MT 533 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:37,5:33.0:42:0.119:2 0:28,0:.:28:0.0:0 -MT 4917 rs28357980 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:18,17:31.0:35:0.486:2 0:28,0:.:28:0.0:0 -MT 16019 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:20,3:32.0:23:0.13:2 0:15,0:.:15:0.0:0 -MT 16163 rs41479950 A G . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:18,9:32.0:27:0.333:2 0:25,0:.:25:0.0:0 -MT 16186 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:23,9:31.0:32:0.281:2 0:23,0:.:23:0.0:0 -MT 16263 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:20,27:32.0:47:0.574:2 0:22,0:.:22:0.0:0 -MT 16316 . A G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:19,24:31.0:43:0.558:2 0:20,0:.:20:0.0:0 -GL000220.1 119409 . C T . PASS . GT:AD:BQ:DP:FA 0/1:45,6:21.0:51:0.118 0:84,3:.:87:0.034 -GL000220.1 119911 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:22,5:29.0:27:0.185:2 0:36,0:.:37:0.0:0 -GL000220.1 119967 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:31,4:32.0:35:0.114:2 0:48,1:.:49:0.02:0 -GL000220.1 119970 . C T . PASS . GT:AD:BQ:DP:FA 0/1:29,8:29.0:37:0.216 0:44,4:.:49:0.083 -GL000220.1 120319 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:22,3:30.0:25:0.12:2 0:33,1:.:34:0.029:0 -GL000220.1 125098 . C G . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:23,4:31.0:27:0.148:2 0:47,1:.:48:0.021:0 -GL000220.1 126307 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:10,6:31.0:16:0.375:2 0:14,0:.:14:0.0:0 -GL000220.1 133613 . T A . PASS . GT:AD:BQ:DP:FA 0/1:73,7:26.0:80:0.088 0:97,0:.:99:0.0 -GL000220.1 137741 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:79,6:29.0:85:0.071:2 0:77,0:.:77:0.0:0 +1 4955833 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:128,12:30.0:140:0.086:2 0:179,0:.:179:0.0:0 +1 11181985 rs41274510 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:165,32:30.0:197:0.162:2 0:173,0:.:173:0.0:0 +1 11317260 . G A . PASS FAILURE_REASON=possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:194,5:29.0:200:0.025 0:217,0:.:217:0.0 +1 14192818 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:32,8:31.0:40:0.2:2 0:35,0:.:36:0.0:0 +1 16258302 rs113470169 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:276,215:32.0:492:0.438 0:537,22:.:559:0.039 +1 16972793 . T A . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:336,23:29.0:359:0.064 0:325,0:.:325:0.0 +1 16974817 rs199598697 C G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:543,247:31.0:791:0.313 0:794,20:.:815:0.025 +1 16975228 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:3451,138:30.0:3594:0.038:2 0:3270,1:.:3273:0.0003057:0 +1 17087395 . G A . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:3103,31:29.0:3136:0.009892 0:2283,4:.:2288:0.001749 +1 23880912 rs34671368 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:66,170:30.0:236:0.72 0:285,8:.:293:0.027 +1 23881005 rs35140318 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:209,639:31.0:848:0.754 0:1001,24:.:1025:0.023 +1 27533368 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:159,19:30.0:178:0.107:2 0:224,0:.:224:0.0:0 +1 36824305 rs145929365 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:439,74:30.0:513:0.144:2 0:480,0:.:481:0.0:0 +1 45798981 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:647,24:28.0:671:0.036:2 0:656,1:.:657:0.001522:0 +1 46509146 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:6,5:31.0:11:0.455:2 0:12,0:.:12:0.0:0 +1 46740500 rs75959881 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:79,8:32.0:87:0.092:2 0:77,0:.:77:0.0:0 +1 51436157 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:317,12:29.0:329:0.036:2 0:363,0:.:363:0.0:0 +1 51439777 rs1043141 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:301,63:30.0:364:0.173 0:404,11:.:416:0.027 +1 59250675 rs17265089 C G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:884,187:32.0:1073:0.175 0:1046,26:.:1072:0.024 +1 65321028 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,3:33.0:23:0.136:2 0:15,0:.:15:0.0:0 +1 65332766 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:475,20:30.0:497:0.04:2 0:476,0:.:476:0.0:0 +1 65349304 rs72675459 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:35,10:31.0:45:0.222:2 0:32,0:.:32:0.0:0 +1 65351748 rs112941888 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:47,7:31.0:54:0.13:2 0:47,0:.:47:0.0:0 +1 69777307 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:9,3:32.0:12:0.25:2 0:15,0:.:15:0.0:0 +1 72058827 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:43,6:31.0:49:0.122:2 0:34,0:.:34:0.0:0 +1 72748280 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=clustered_read_position GT:AD:BQ:DP:FA:SS 0/1:74,22:30.0:96:0.229:2 0:172,0:.:172:0.0:0 +1 84971819 rs76421103 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:16,5:28.0:21:0.238:2 0:22,0:.:22:0.0:0 +1 85739861 rs12563515 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:77,31:32.0:108:0.287 0:73,4:.:77:0.052 +1 85741968 rs12562182 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1005,50:32.0:1056:0.047:2 0:1248,0:.:1250:0.0:0 +1 85742157 rs1060843 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:229,10:30.0:242:0.042:2 0:227,0:.:227:0.0:0 +1 101971074 rs404156 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:36,11:30.0:47:0.234:2 0:52,0:.:52:0.0:0 +1 117753543 rs61759536 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:279,44:30.0:323:0.136:2 0:244,0:.:244:0.0:0 +1 118166096 rs2884587 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:709,150:30.0:859:0.175 0:701,19:.:722:0.026 +1 118166750 rs2066411 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:31,19:30.0:50:0.38:2 0:23,0:.:23:0.0:0 +1 120429402 rs74115384 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:72,5:33.0:77:0.065:2 0:51,0:.:51:0.0:0 +1 120468134 rs6692009 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:626,133:30.0:760:0.175:2 0:579,0:.:579:0.0:0 +1 120468487 rs6658796 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:98,29:29.0:127:0.228:2 0:127,0:.:128:0.0:0 +1 149857797 rs202141121 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:45,15:32.0:60:0.25:2 0:43,0:.:43:0.0:0 +1 152330829 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:147,65:30.0:212:0.307:2 0:112,0:.:112:0.0:0 +1 152331013 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:153,21:31.0:174:0.121:2 0:88,0:.:88:0.0:0 +1 156785653 . C G . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:875,31:32.0:910:0.034 0:636,0:.:637:0.0 +1 156848778 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:92,18:29.0:110:0.164:2 0:37,0:.:37:0.0:0 +1 156849047 rs142870382 G T . PASS DB;FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:987,20:30.0:1008:0.02 0:518,0:.:519:0.0 +1 156849658 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:89,11:31.0:100:0.11:2 0:26,0:.:26:0.0:0 +1 157599882 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:142,18:31.0:160:0.113:2 0:139,0:.:139:0.0:0 +1 162737241 rs75932087 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:149,18:29.0:167:0.108:2 0:68,0:.:68:0.0:0 +1 162740121 rs34722354 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:577,206:29.0:783:0.263 0:500,25:.:525:0.048 +1 165044147 rs34089781 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:38,53:31.0:91:0.582:2 0:59,0:.:59:0.0:0 +1 175958637 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:386,15:29.0:401:0.037:2 0:246,0:.:247:0.0:0 +1 176175885 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:176,10:31.0:186:0.054:2 0:102,0:.:102:0.0:0 +1 181819202 rs190395201 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:55,14:30.0:69:0.203:2 0:37,0:.:37:0.0:0 +1 184327323 rs6665185 T G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:159,60:31.0:219:0.274:2 0:107,0:.:108:0.0:0 +1 185520654 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:458,19:31.0:478:0.04:2 0:206,0:.:206:0.0:0 +1 193091490 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:579,16:30.0:596:0.027:2 0:313,0:.:313:0.0:0 +1 193104712 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:492,106:30.0:598:0.177:2 0:364,0:.:364:0.0:0 +1 193203268 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:381,19:30.0:402:0.048:2 0:221,0:.:222:0.0:0 +1 204495610 . G T . PASS FAILURE_REASON=clustered_read_position GT:AD:BQ:DP:FA 0/1:158,7:27.0:166:0.042 0:158,1:.:163:0.006289 +1 206648147 rs1953090 T G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:235,99:30.0:335:0.296 0:170,8:.:178:0.045 +1 206650065 rs41296034 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:589,200:32.0:789:0.253:2 0:530,0:.:530:0.0:0 +1 206944936 . T C . PASS FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:48,3:33.0:51:0.059 0:16,0:.:16:0.0 +1 221053574 rs62621984 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:67,5:33.0:72:0.069:2 0:61,0:.:61:0.0:0 +1 226562112 rs1805401 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:230,60:32.0:290:0.207:2 0:157,0:.:157:0.0:0 +1 226567172 rs2271345 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:171,57:30.0:228:0.25 0:116,6:.:123:0.049 +1 228617397 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:303,45:28.0:348:0.129:2 0:120,0:.:120:0.0:0 +1 230355441 rs12061439 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:227,79:30.0:306:0.258:2 0:200,0:.:200:0.0:0 +1 241663941 . C G . PASS FAILURE_REASON=possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:236,4:30.0:241:0.017 0:96,0:.:96:0.0 +1 247555079 rs114193294 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:25,11:32.0:36:0.306:2 0:20,0:.:20:0.0:0 +2 6636119 rs147273945 T A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:604,28:30.0:633:0.044 0:440,4:.:444:0.009009 +2 6636414 rs183255044 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:695,42:30.0:737:0.057:2 0:502,0:.:502:0.0:0 +2 6636735 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:479,18:30.0:498:0.036:2 0:318,0:.:318:0.0:0 +2 7541718 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:114,38:30.0:153:0.25:2 0:153,0:.:154:0.0:0 +2 14528089 rs147905894 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:285,33:30.0:319:0.104:2 0:221,0:.:222:0.0:0 +2 16085519 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:84,8:31.0:92:0.087:2 0:34,0:.:34:0.0:0 +2 25466810 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:745,27:30.0:773:0.035:2 0:616,0:.:619:0.0:0 +2 25972936 rs192716734 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:721,54:29.0:778:0.07:2 0:581,0:.:582:0.0:0 +2 27014885 rs143726653 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:166,10:27.0:176:0.057:2 0:108,0:.:108:0.0:0 +2 29429948 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:274,49:31.0:323:0.152:2 0:185,1:.:186:0.005376:0 +2 29451986 rs62130588 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:316,17:28.0:333:0.051:2 0:165,0:.:165:0.0:0 +2 29519851 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:810,36:31.0:846:0.043:2 0:649,1:.:651:0.001538:0 +2 29940332 rs116369425 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:84,12:31.0:96:0.125:2 0:51,0:.:51:0.0:0 +2 43952068 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:52,9:30.0:61:0.148:2 0:51,0:.:51:0.0:0 +2 46128526 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:289,32:31.0:321:0.1:2 0:173,0:.:174:0.0:0 +2 47630213 rs2303425 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:73,51:32.0:125:0.411 0:61,3:.:64:0.047 +2 47630314 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:404,32:31.0:436:0.073:2 0:328,0:.:328:0.0:0 +2 47693788 rs12998837 A T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:269,165:29.0:434:0.38 0:291,21:.:312:0.067 +2 47708075 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:125,31:30.0:157:0.199:2 0:111,0:.:111:0.0:0 +2 47709807 rs6737098 T A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:108,21:30.0:129:0.163:2 0:54,1:.:55:0.018:0 +2 47905398 rs182017009 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:459,125:29.0:584:0.214:2 0:537,1:.:538:0.001859:0 +2 48025764 rs1800937 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:262,97:31.0:359:0.27 0:361,18:.:379:0.047 +2 48030629 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:906,51:30.0:957:0.053:2 0:966,0:.:967:0.0:0 +2 51288710 rs34304690 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:545,378:32.0:924:0.41 0:639,44:.:683:0.064 +2 54660484 rs17045894 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:269,25:30.0:294:0.085:2 0:226,1:.:227:0.004405:0 +2 61108926 rs147771199 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:157,87:32.0:245:0.357:2 0:265,0:.:265:0.0:0 +2 61710320 rs113262337 T A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:86,6:32.0:92:0.065:2 0:68,0:.:68:0.0:0 +2 61760814 rs115819167 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:172,23:30.0:195:0.118:2 0:140,0:.:140:0.0:0 +2 67049381 rs61743348 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:298,58:31.0:356:0.163:2 0:208,0:.:208:0.0:0 +2 79524994 rs72917249 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:129,165:30.0:294:0.561:2 0:221,0:.:221:0.0:0 +2 81424759 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1231,153:31.0:1384:0.111:2 0:979,0:.:979:0.0:0 +2 81425558 . C T . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:1519,19:30.0:1539:0.012 0:1060,0:.:1062:0.0 +2 81425585 rs112215672 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:1033,462:30.0:1500:0.309 0:989,47:.:1037:0.045 +2 81426909 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1279,451:30.0:1732:0.261:2 0:1210,0:.:1213:0.0:0 +2 81427308 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:730,304:30.0:1034:0.294:2 0:714,0:.:714:0.0:0 +2 99160361 rs2230387 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:621,43:31.0:664:0.065:2 0:532,0:.:535:0.0:0 +2 106021437 rs72945057 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:234,38:31.0:272:0.14:2 0:217,0:.:217:0.0:0 +2 111881810 rs72948328 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:55,18:30.0:73:0.247 0:61,3:.:65:0.047 +2 111885565 rs116747219 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:140,37:31.0:177:0.209:2 0:162,0:.:162:0.0:0 +2 111909610 rs79493742 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:75,7:32.0:82:0.085:2 0:48,1:.:49:0.02:0 +2 113978894 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:290,140:30.0:431:0.326:2 0:340,1:.:342:0.002933:0 +2 113979364 rs72831810 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:328,57:30.0:385:0.148 0:315,7:.:322:0.022 +2 113981691 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:525,21:31.0:546:0.038:2 0:514,1:.:515:0.001942:0 +2 121735983 rs169430 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:214,18:29.0:232:0.078:2 0:195,0:.:195:0.0:0 +2 128038005 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:383,20:31.0:403:0.05:2 0:367,0:.:367:0.0:0 +2 131950767 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:227,99:32.0:326:0.304:2 0:265,0:.:265:0.0:0 +2 136869825 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:49,4:31.0:53:0.075:2 0:23,0:.:23:0.0:0 +2 158617379 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:807,197:31.0:1004:0.196:2 0:919,0:.:919:0.0:0 +2 158622572 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1313,113:30.0:1426:0.079:2 0:1094,1:.:1098:0.0009132:0 +2 158655838 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:232,19:32.0:251:0.076:2 0:177,0:.:177:0.0:0 +2 173914884 rs56306605 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:48,12:33.0:60:0.2:2 0:43,1:.:44:0.023:0 +2 180265135 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:381,68:31.0:449:0.151:2 0:439,0:.:439:0.0:0 +2 180265174 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:478,100:30.0:578:0.173:2 0:578,1:.:579:0.001727:0 +2 184373044 rs140832966 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:10,5:31.0:15:0.333:2 0:27,0:.:27:0.0:0 +2 189541807 rs7579655 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:35,13:32.0:48:0.271:2 0:38,0:.:38:0.0:0 +2 190708712 rs2066459 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:597,118:30.0:715:0.165:2 0:563,0:.:563:0.0:0 +2 190718940 rs5743137 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:137,64:32.0:201:0.318:2 0:190,0:.:190:0.0:0 +2 198257008 rs72912888 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:137,91:32.0:228:0.399:2 0:192,0:.:192:0.0:0 +2 198266602 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:376,29:30.0:406:0.072:2 0:378,0:.:379:0.0:0 +2 198285583 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:11,3:32.0:14:0.214:2 0:8,0:.:8:0.0:0 +2 202137781 rs200682299 C T . PASS DB;FAILURE_REASON=nearby_gap_events,clustered_read_position GT:AD:BQ:DP:FA 0/1:63,8:17.0:71:0.113 0:71,5:.:76:0.066 +2 202149589 rs1045485 G C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:404,69:32.0:474:0.146 0:535,13:.:550:0.024 +2 212426588 rs139728050 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:319,34:30.0:353:0.096:2 0:390,0:.:391:0.0:0 +2 212522450 rs35497618 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:182,111:30.0:293:0.379:2 0:379,0:.:380:0.0:0 +2 212522651 rs34621071 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:350,145:31.0:495:0.293:2 0:560,0:.:560:0.0:0 +2 212578523 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:22,6:30.0:28:0.214:2 0:20,0:.:20:0.0:0 +2 212589774 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:218,18:32.0:236:0.076:2 0:258,0:.:258:0.0:0 +2 212698775 rs714394 T A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:95,95:31.0:190:0.5 0:160,11:.:171:0.064 +2 212812057 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:117,17:29.0:134:0.127:2 0:85,0:.:85:0.0:0 +2 225069340 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:154,14:30.0:168:0.083:2 0:156,0:.:156:0.0:0 +2 226701540 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:27,6:33.0:33:0.182:2 0:38,0:.:38:0.0:0 +3 12028100 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:18,4:30.0:22:0.182:2 0:8,0:.:8:0.0:0 +3 25569630 rs73048042 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:71,46:29.0:117:0.393:2 0:153,0:.:153:0.0:0 +3 29047705 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:94,9:31.0:103:0.087:2 0:138,0:.:138:0.0:0 +3 30713834 rs35766612 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:514,26:30.0:540:0.048:2 0:629,1:.:630:0.001587:0 +3 37034946 rs1800734 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:44,54:27.0:98:0.551 0:110,5:.:115:0.043 +3 37050254 rs4647255 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:106,60:31.0:166:0.361 0:149,5:.:154:0.032 +3 37061720 rs104894999 G C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:101,46:31.0:147:0.313 0:121,6:.:127:0.047 +3 41266226 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:402,23:32.0:426:0.054:2 0:424,0:.:425:0.0:0 +3 41275350 rs3856748 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:157,141:30.0:300:0.473:2 0:290,0:.:291:0.0:0 +3 41443220 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:248,13:31.0:261:0.05:2 0:288,0:.:288:0.0:0 +3 47061453 rs10510752 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:37,31:29.0:68:0.456:2 0:64,0:.:64:0.0:0 +3 47098278 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:179,55:32.0:234:0.235:2 0:222,1:.:224:0.004484:0 +3 48515221 rs187202071 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:9,9:30.0:18:0.5:2 0:29,0:.:29:0.0:0 +3 52436441 rs149499021 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:201,159:31.0:360:0.442:2 0:248,0:.:248:0.0:0 +3 52663084 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:125,14:31.0:139:0.101:2 0:173,0:.:173:0.0:0 +3 55487222 rs11709866 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:180,8:30.0:188:0.043:2 0:181,0:.:181:0.0:0 +3 69988437 . G T . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:40,6:20.0:46:0.13 0:42,0:.:42:0.0 +3 70005712 rs55754687 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:310,17:32.0:328:0.052:2 0:314,1:.:315:0.003175:0 +3 71007294 . G C . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:140,13:18.0:156:0.085 0:144,2:.:149:0.014 +3 71019797 rs139128497 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:93,51:31.0:144:0.354:2 0:182,0:.:182:0.0:0 +3 71246918 rs2293137 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:16,15:30.0:31:0.484:2 0:34,0:.:34:0.0:0 +3 71247014 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:185,7:32.0:192:0.036:2 0:214,0:.:214:0.0:0 +3 71247304 rs2037474 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:174,109:32.0:283:0.385 0:302,20:.:322:0.062 +3 72323080 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:132,17:31.0:149:0.114:2 0:199,0:.:199:0.0:0 +3 72323287 rs35092991 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:86,63:31.0:149:0.423 0:129,8:.:137:0.058 +3 75164938 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:40,38:28.0:78:0.487:2 0:105,0:.:105:0.0:0 +3 87347973 rs2646219 G T . PASS DB;FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:42,3:31.0:45:0.067 0:56,0:.:56:0.0 +3 89905902 rs58068122 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:63,36:31.0:99:0.364:2 0:84,0:.:84:0.0:0 +3 94429115 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:482,39:33.0:521:0.075:2 0:450,0:.:451:0.0:0 +3 106824274 rs16834059 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:122,86:30.0:208:0.413 0:178,7:.:185:0.038 +3 106824304 rs114734174 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:130,95:30.0:225:0.422 0:178,11:.:191:0.058 +3 106825024 rs7628252 G C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:138,140:31.0:278:0.504 0:239,20:.:259:0.077 +3 106825180 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:571,30:31.0:601:0.05:2 0:514,0:.:514:0.0:0 +3 117078556 rs116733551 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:24,5:34.0:29:0.172:2 0:34,0:.:34:0.0:0 +3 117078561 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:14,13:30.0:27:0.481:2 0:35,0:.:35:0.0:0 +3 128199913 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:478,161:30.0:641:0.252:2 0:428,0:.:428:0.0:0 +3 134670080 rs77546042 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:88,19:30.0:107:0.178:2 0:44,0:.:45:0.0:0 +3 134851577 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:548,70:31.0:618:0.113:2 0:482,0:.:482:0.0:0 +3 134884695 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:96,25:32.0:121:0.207:2 0:65,0:.:65:0.0:0 +3 134885042 rs9866044 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:91,40:32.0:131:0.305:2 0:58,0:.:58:0.0:0 +3 134967265 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:648,24:30.0:673:0.036 0:598,2:.:600:0.003333 +3 135644964 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:152,26:30.0:178:0.146:2 0:159,0:.:159:0.0:0 +3 137443260 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:29,5:27.0:34:0.147:2 0:37,0:.:37:0.0:0 +3 138374293 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:605,34:30.0:641:0.053:2 0:618,0:.:619:0.0:0 +3 138663179 rs2291251 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:399,183:32.0:582:0.314:2 0:556,0:.:557:0.0:0 +3 142188172 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:245,34:30.0:279:0.122:2 0:255,0:.:255:0.0:0 +3 142215149 rs74677466 T C . PASS DB;FAILURE_REASON=nearby_gap_events,alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:111,31:32.0:142:0.218 0:89,3:.:92:0.033 +3 142215151 . T C . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:124,21:32.0:145:0.145 0:96,1:.:98:0.01 +3 142215153 . T C . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:140,5:32.0:145:0.034 0:103,0:.:103:0.0 +3 142218675 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:73,8:29.0:81:0.099:2 0:58,0:.:58:0.0:0 +3 142266439 rs13091637 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:23,30:30.0:53:0.566:2 0:28,0:.:28:0.0:0 +3 142278101 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:350,123:32.0:473:0.26:2 0:454,0:.:454:0.0:0 +3 178511531 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:251,15:29.0:266:0.056:2 0:219,0:.:219:0.0:0 +3 178927345 rs3729682 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:295,12:31.0:307:0.039:2 0:221,1:.:222:0.004505:0 +3 178936227 rs17849071 T G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:84,5:31.0:89:0.056:2 0:41,0:.:41:0.0:0 +3 185183491 rs192528458 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:214,97:30.0:311:0.312:2 0:277,0:.:277:0.0:0 +3 185183656 rs201265411 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:238,127:30.0:365:0.348:2 0:350,1:.:351:0.002849:0 +3 186504406 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:907,63:33.0:971:0.065:2 0:1005,0:.:1007:0.0:0 +3 187440126 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:61,6:26.0:67:0.09:2 0:37,0:.:38:0.0:0 +3 187451349 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:694,22:31.0:717:0.031:2 0:584,0:.:584:0.0:0 +3 189349501 rs13064999 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:56,54:31.0:110:0.491:2 0:70,1:.:71:0.014:0 +3 189525985 rs141006314 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:279,12:29.0:291:0.041:2 0:203,0:.:203:0.0:0 +3 189525986 rs149767941 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:283,12:31.0:295:0.041:2 0:207,0:.:207:0.0:0 +3 189584420 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:190,31:30.0:221:0.14:2 0:164,0:.:165:0.0:0 +3 189586466 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:369,18:30.0:387:0.047:2 0:333,0:.:334:0.0:0 +3 189586470 rs147148566 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:270,111:30.0:381:0.291:2 0:326,0:.:327:0.0:0 +3 189590871 rs111843185 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:147,52:30.0:199:0.261:2 0:124,0:.:125:0.0:0 +3 189597951 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:587,193:30.0:780:0.247 0:688,3:.:691:0.004342 +3 189598095 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:86,14:29.0:100:0.14:2 0:38,0:.:38:0.0:0 +3 195399620 rs9840981 C G . PASS DB;FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:187,153:32.0:341:0.45 0:113,22:.:135:0.163 +3 195399678 rs9874761 G T . PASS DB;FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:72,72:30.0:144:0.5 0:33,21:.:54:0.389 +3 195410875 rs201763651 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:163,53:28.0:216:0.245:2 0:74,0:.:74:0.0:0 +3 197346530 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:125,20:32.0:145:0.138:2 0:86,0:.:87:0.0:0 +4 1795762 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:442,39:30.0:481:0.081:2 0:317,1:.:318:0.003145:0 +4 1806937 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:85,21:31.0:107:0.198:2 0:35,0:.:35:0.0:0 +4 6113451 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:123,16:31.0:139:0.115:2 0:91,0:.:92:0.0:0 +4 20891334 . A T . PASS FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:38,3:31.0:41:0.073 0:21,0:.:21:0.0 +4 21650176 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:32,3:32.0:35:0.086:2 0:13,0:.:13:0.0:0 +4 28400468 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:132,26:31.0:158:0.165:2 0:113,0:.:113:0.0:0 +4 35861432 rs181017058 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:18,7:30.0:25:0.28:2 0:38,0:.:38:0.0:0 +4 41747691 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:14,4:32.0:18:0.222:2 0:13,0:.:13:0.0:0 +4 41748217 rs17885216 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:723,80:29.0:803:0.1 0:971,5:.:976:0.005123 +4 46726267 . C T . PASS FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:420,77:30.0:497:0.155 0:516,2:.:519:0.003861 +4 54245372 . T A . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:332,5:31.0:337:0.015 0:415,0:.:415:0.0 +4 55129831 rs55947416 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:281,196:30.0:478:0.411:2 0:471,0:.:471:0.0:0 +4 55138785 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:29,3:32.0:32:0.094:2 0:34,0:.:35:0.0:0 +4 55979609 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:532,41:30.0:573:0.072 0:622,2:.:624:0.003205 +4 65604620 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:85,43:29.0:128:0.336:2 0:115,0:.:115:0.0:0 +4 66189753 rs67487372 C T . PASS DB;FAILURE_REASON=nearby_gap_events,possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:263,7:31.0:270:0.026 0:241,1:.:243:0.004132 +4 66218677 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:332,22:30.0:354:0.062:2 0:294,0:.:294:0.0:0 +4 66270345 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:36,7:31.0:43:0.163:2 0:14,0:.:14:0.0:0 +4 66286376 rs116596375 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:89,9:30.0:98:0.092:2 0:65,1:.:66:0.015:0 +4 78271554 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:180,10:32.0:191:0.053:2 0:201,0:.:202:0.0:0 +4 87163541 rs114515845 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:22,4:27.0:26:0.154:2 0:19,0:.:19:0.0:0 +4 120324304 . C T . PASS FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:69,8:30.0:77:0.104 0:76,0:.:76:0.0 +4 143043397 rs34561493 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:265,73:30.0:338:0.216 0:347,10:.:358:0.028 +4 143158979 rs28647625 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:106,82:31.0:188:0.436 0:162,3:.:165:0.018 +4 153245521 . C G . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:414,8:33.0:423:0.019 0:401,0:.:402:0.0 +4 166144830 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:269,22:32.0:291:0.076:2 0:337,0:.:337:0.0:0 +4 175047618 rs2196386 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:117,69:31.0:186:0.371 0:165,12:.:177:0.068 +4 182443933 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:206,30:32.0:236:0.127:2 0:371,0:.:371:0.0:0 +4 182444093 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:250,32:31.0:282:0.113:2 0:488,0:.:488:0.0:0 +4 182444132 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:125,75:31.0:200:0.375:2 0:338,1:.:340:0.00295:0 +4 187509875 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:281,45:30.0:326:0.138:2 0:436,0:.:436:0.0:0 +4 187527089 rs184407616 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:36,13:31.0:49:0.265:2 0:58,0:.:58:0.0:0 +4 187531022 rs28647489 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:344,101:31.0:445:0.227:2 0:537,1:.:538:0.001859:0 +4 187540042 rs192818736 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:479,52:30.0:531:0.098:2 0:642,1:.:643:0.001555:0 +4 187541598 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:409,13:29.0:422:0.031:2 0:450,0:.:450:0.0:0 +4 187542755 rs28489116 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:462,140:32.0:602:0.233:2 0:641,1:.:642:0.001558:0 +4 187542922 rs34360279 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:255,31:30.0:286:0.108:2 0:283,0:.:283:0.0:0 +4 187542986 rs28423024 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:85,34:32.0:119:0.286:2 0:107,0:.:107:0.0:0 +4 187557113 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:173,12:32.0:185:0.065:2 0:160,0:.:160:0.0:0 +4 187584530 rs200633985 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:452,54:30.0:506:0.107:2 0:470,1:.:472:0.002123:0 +4 187628352 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:190,81:30.0:271:0.299:2 0:329,0:.:330:0.0:0 +4 190093234 rs72727625 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:83,152:31.0:235:0.647 0:297,7:.:307:0.023 +5 240664 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=clustered_read_position GT:AD:BQ:DP:FA:SS 0/1:108,83:32.0:191:0.435:2 0:78,0:.:78:0.0:0 +5 1255297 rs113604559 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:152,13:30.0:165:0.079:2 0:50,0:.:50:0.0:0 +5 1272414 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:530,157:30.0:687:0.229 0:287,4:.:291:0.014 +5 1280190 rs147103794 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:338,97:30.0:435:0.223:2 0:164,0:.:164:0.0:0 +5 1293389 rs79662648 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:249,136:31.0:385:0.353:2 0:130,0:.:130:0.0:0 +5 1295250 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:644,199:29.0:845:0.236:2 0:368,0:.:369:0.0:0 +5 1576000 rs148387081 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:174,18:30.0:192:0.094:2 0:76,0:.:76:0.0:0 +5 17491448 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:332,99:28.0:431:0.23:2 0:221,0:.:221:0.0:0 +5 17670396 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:623,17:30.0:641:0.027:2 0:357,0:.:357:0.0:0 +5 22934638 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:89,6:28.0:95:0.063:2 0:55,0:.:55:0.0:0 +5 23303757 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:824,74:30.0:898:0.082:2 0:461,0:.:461:0.0:0 +5 23303943 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:800,44:30.0:844:0.052:2 0:434,0:.:434:0.0:0 +5 23304880 rs78261567 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:618,115:32.0:733:0.157:2 0:357,0:.:357:0.0:0 +5 26670194 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:195,12:29.0:207:0.058:2 0:65,0:.:65:0.0:0 +5 33997307 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:243,14:31.0:257:0.054:2 0:104,0:.:104:0.0:0 +5 35860873 rs148287783 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:109,51:29.0:160:0.319:2 0:97,0:.:97:0.0:0 +5 35871291 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:464,58:31.0:522:0.111:2 0:371,1:.:372:0.002688:0 +5 35875518 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:133,33:29.0:166:0.199:2 0:96,0:.:96:0.0:0 +5 38942628 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:49,6:32.0:55:0.109:2 0:22,0:.:22:0.0:0 +5 38947185 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:26,9:31.0:35:0.257:2 0:17,0:.:17:0.0:0 +5 38949632 rs116407384 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:116,36:29.0:152:0.237:2 0:68,0:.:68:0.0:0 +5 38962656 . T C . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:696,9:30.0:706:0.013 0:478,0:.:478:0.0 +5 40457488 rs112491400 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:385,20:30.0:405:0.049:2 0:255,1:.:256:0.003906:0 +5 52665368 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:215,10:31.0:225:0.044:2 0:212,0:.:212:0.0:0 +5 56168571 rs2053696 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:153,115:30.0:268:0.429:2 0:370,0:.:371:0.0:0 +5 62835420 rs13165927 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:22,9:32.0:31:0.29:2 0:39,1:.:40:0.025:0 +5 62836591 rs13153547 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:31,22:31.0:53:0.415:2 0:41,1:.:42:0.024:0 +5 62836726 rs13153708 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:159,142:30.0:302:0.472 0:329,9:.:339:0.027 +5 67569342 rs3730078 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:296,13:33.0:309:0.042:2 0:297,0:.:298:0.0:0 +5 79172158 rs77646428 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:170,20:30.0:190:0.105:2 0:156,0:.:156:0.0:0 +5 112043283 rs182500056 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:81,9:30.0:90:0.1:2 0:63,0:.:63:0.0:0 +5 112175617 rs67622085 T A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:550,67:30.0:619:0.109:2 0:825,1:.:828:0.001211:0 +5 112213686 . G C . PASS FAILURE_REASON=nearby_gap_events,possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:221,6:28.0:228:0.026 0:369,0:.:370:0.0 +5 112227998 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:929,60:30.0:989:0.061:2 0:1057,1:.:1059:0.0009452:0 +5 140256920 rs115718636 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:118,158:32.0:276:0.572:2 0:236,0:.:237:0.0:0 +5 149460627 rs201114404 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:218,18:31.0:236:0.076:2 0:124,0:.:124:0.0:0 +5 149502838 rs56388645 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:96,114:30.0:210:0.543:2 0:91,0:.:91:0.0:0 +5 170828123 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:24,4:32.0:28:0.143:2 0:28,0:.:28:0.0:0 +5 176516631 rs1966265 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:403,131:31.0:534:0.245 0:542,2:.:544:0.003676 +5 176517801 rs55701137 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:846,36:31.0:882:0.041:2 0:688,0:.:688:0.0:0 +5 176524465 rs146820395 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:705,35:29.0:740:0.047:2 0:542,1:.:543:0.001842:0 +5 176636546 rs201076688 G A . PASS DB;FAILURE_REASON=nearby_gap_events,alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:28,28:27.0:56:0.5 0:98,4:.:104:0.039 +5 176637149 rs3733874 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:102,223:30.0:325:0.686 0:344,10:.:354:0.028 +5 176637240 rs3733875 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:160,294:30.0:456:0.648 0:433,14:.:447:0.031 +5 176637576 rs28932178 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:132,220:32.0:352:0.625 0:333,11:.:344:0.032 +5 178996554 rs115920408 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:16,28:30.0:44:0.636:2 0:26,0:.:26:0.0:0 +5 180046427 rs141303558 C T . PASS DB;FAILURE_REASON=possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:300,7:29.0:307:0.023 0:222,1:.:223:0.004484 +5 180046494 . G C . PASS FAILURE_REASON=nearby_gap_events,alt_allele_in_normal,clustered_read_position GT:AD:BQ:DP:FA 0/1:4,6:32.0:10:0.6 0:102,2:.:105:0.019 +6 6728616 rs9504905 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:10,16:31.0:26:0.615:2 0:20,0:.:20:0.0:0 +6 20486794 rs3763279 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:61,7:28.0:68:0.103:2 0:46,0:.:46:0.0:0 +6 25261662 rs113389452 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:102,58:30.0:160:0.363:2 0:140,0:.:140:0.0:0 +6 25606672 rs742130 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:188,96:30.0:284:0.338 0:194,11:.:207:0.054 +6 26031720 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:61,14:31.0:76:0.187:2 0:36,0:.:36:0.0:0 +6 26322501 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:126,42:30.0:168:0.25:2 0:136,0:.:136:0.0:0 +6 27840221 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:194,13:31.0:207:0.063:2 0:125,0:.:125:0.0:0 +6 29236588 rs17344111 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:82,35:32.0:117:0.299 0:86,4:.:90:0.044 +6 29693183 rs150767875 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:227,94:30.0:321:0.293:2 0:240,0:.:241:0.0:0 +6 29760132 rs114179071 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:198,93:29.0:291:0.32:2 0:195,0:.:197:0.0:0 +6 29760317 rs61737605 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:102,36:31.0:138:0.261:2 0:103,0:.:103:0.0:0 +6 29760462 rs61729757 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:140,22:32.0:162:0.136:2 0:165,0:.:165:0.0:0 +6 29760765 rs115583841 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:331,90:30.0:421:0.214:2 0:374,0:.:374:0.0:0 +6 29760799 rs77141969 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:247,76:30.0:323:0.235:2 0:291,0:.:292:0.0:0 +6 29760856 rs116510017 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:133,65:29.0:198:0.328:2 0:128,0:.:128:0.0:0 +6 29769246 rs9468626 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:69,34:30.0:103:0.33:2 0:79,0:.:79:0.0:0 +6 29795566 rs17875397 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:292,117:29.0:409:0.286:2 0:261,1:.:262:0.003817:0 +6 29795913 rs41551813 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:318,121:31.0:439:0.276:2 0:263,0:.:263:0.0:0 +6 29796106 rs17875399 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:320,38:30.0:360:0.106:2 0:304,0:.:305:0.0:0 +6 29796265 rs17875401 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:91,38:30.0:129:0.295:2 0:53,0:.:53:0.0:0 +6 29796675 rs17875404 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:41,14:30.0:55:0.255:2 0:26,0:.:26:0.0:0 +6 29797155 rs17875405 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:171,81:31.0:252:0.321:2 0:166,0:.:166:0.0:0 +6 29797211 rs41562616 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:250,119:31.0:369:0.322:2 0:251,0:.:252:0.0:0 +6 29902040 rs1611306 A G . PASS DB;FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:148,37:31.0:185:0.2 0:109,32:.:141:0.227 +6 29910856 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:334,30:30.0:364:0.082:2 0:276,0:.:276:0.0:0 +6 29912149 rs114818671 G C . PASS DB;FAILURE_REASON=alt_allele_in_normal,clustered_read_position GT:AD:BQ:DP:FA 0/1:910,241:31.0:1152:0.209 0:798,44:.:842:0.052 +6 29912852 rs1137296 T C . PASS DB;FAILURE_REASON=possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:635,113:32.0:748:0.151 0:382,214:.:597:0.359 +6 29925438 rs11757135 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:176,76:30.0:252:0.302 0:177,7:.:184:0.038 +6 30459165 rs62621992 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:321,33:31.0:354:0.093:2 0:335,0:.:335:0.0:0 +6 30670292 rs9405048 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:523,20:31.0:543:0.037:2 0:441,1:.:442:0.002262:0 +6 30672326 rs17292678 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:806,480:30.0:1286:0.373 0:990,60:.:1051:0.057 +6 30865204 rs2267641 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:54,14:33.0:68:0.206 0:71,3:.:74:0.041 +6 31238068 rs1050276 C T . PASS DB;FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:25,11:29.0:36:0.306 0:68,4:.:72:0.056 +6 31239050 rs713032 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:93,85:29.0:203:0.478 0:137,42:.:294:0.235 +6 31239602 rs1050441 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:182,53:30.0:235:0.226 0:330,23:.:353:0.065 +6 31322205 rs151341416 A C . PASS DB;FAILURE_REASON=nearby_gap_events,alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:15,27:27.0:42:0.643 0:48,7:.:55:0.127 +6 31322209 rs9266106 A G . PASS DB;FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:15,19:23.0:39:0.559 0:41,0:.:59:0.0 +6 31323414 rs41563818 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:277,126:30.0:403:0.313 0:313,3:.:316:0.009494 +6 31324941 rs114038515 C T . PASS DB;FAILURE_REASON=possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:165,4:28.0:170:0.024 0:492,2:.:494:0.004049 +6 32188713 rs8192587 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:379,163:31.0:544:0.301:2 0:352,0:.:353:0.0:0 +6 32188823 rs8192585 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:443,245:30.0:689:0.356:2 0:484,0:.:484:0.0:0 +6 32189192 rs8192584 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:102,35:31.0:137:0.255:2 0:71,0:.:71:0.0:0 +6 32190484 rs8192569 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:255,470:31.0:725:0.648:2 0:552,1:.:555:0.001808:0 +6 33290827 . A T . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:102,5:30.0:107:0.047 0:66,0:.:66:0.0 +6 36650547 rs3176344 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:636,118:31.0:754:0.156:2 0:632,0:.:633:0.0:0 +6 43748328 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:82,56:31.0:140:0.406:2 0:63,0:.:63:0.0:0 +6 58777508 rs4388318 T G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:30,4:33.0:34:0.118:2 0:47,0:.:48:0.0:0 +6 58778828 rs28885508 T A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:25,6:32.0:31:0.194:2 0:48,1:.:49:0.02:0 +6 58779121 rs9500609 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:38,4:28.0:42:0.095:2 0:33,0:.:33:0.0:0 +6 90009220 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:168,14:29.0:182:0.077:2 0:158,0:.:158:0.0:0 +6 93973735 rs138667490 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:243,42:32.0:285:0.147:2 0:183,0:.:183:0.0:0 +6 93973784 . G T . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:127,6:24.0:133:0.045 0:61,0:.:61:0.0 +6 94066446 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1066,55:31.0:1121:0.049:2 0:950,1:.:951:0.001052:0 +6 94068208 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:303,22:32.0:325:0.068:2 0:240,0:.:240:0.0:0 +6 100498638 rs72942225 G T . PASS DB;FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:73,10:29.0:83:0.12 0:51,1:.:52:0.019 +6 100498976 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:113,24:31.0:137:0.175:2 0:138,0:.:138:0.0:0 +6 106051695 rs117032373 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:163,102:31.0:265:0.385:2 0:260,0:.:261:0.0:0 +6 106543620 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:207,46:30.0:253:0.182:2 0:249,1:.:250:0.004:0 +6 106553096 rs143040512 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:653,72:30.0:725:0.099:2 0:650,0:.:650:0.0:0 +6 117639262 rs9282844 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:205,20:29.0:225:0.089 0:162,2:.:164:0.012 +6 117648215 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1013,82:31.0:1096:0.075:2 0:854,0:.:856:0.0:0 +6 117652187 rs518987 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:65,39:30.0:104:0.375 0:69,3:.:72:0.042 +6 117662453 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:625,77:30.0:702:0.11:2 0:527,0:.:527:0.0:0 +6 117665115 rs76141666 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:52,35:30.0:87:0.402 0:44,2:.:46:0.043 +6 117707038 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:290,120:30.0:411:0.293 0:317,2:.:319:0.00627 +6 117724207 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:94,7:30.0:101:0.069:2 0:91,0:.:91:0.0:0 +6 131790227 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:40,4:29.0:44:0.091:2 0:54,0:.:54:0.0:0 +6 136295102 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:63,17:29.0:80:0.213:2 0:45,0:.:45:0.0:0 +6 137519780 rs3799488 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:127,94:30.0:221:0.425 0:213,9:.:222:0.041 +6 137539428 rs201357955 G A . PASS DB;FAILURE_REASON=nearby_gap_events,clustered_read_position GT:AD:BQ:DP:FA 0/1:53,7:30.0:60:0.117 0:67,0:.:67:0.0 +6 137540536 rs17181457 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:132,63:30.0:195:0.323 0:122,5:.:127:0.039 +6 138027910 rs76195386 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:379,103:30.0:482:0.214:2 0:417,0:.:417:0.0:0 +6 138199768 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:577,242:31.0:820:0.295:2 0:828,0:.:829:0.0:0 +6 147728117 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:65,20:30.0:85:0.235:2 0:61,0:.:61:0.0:0 +6 148266586 rs12176381 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:20,35:31.0:55:0.636:2 0:42,1:.:44:0.023:0 +6 152164026 rs9340805 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:99,12:32.0:111:0.108:2 0:73,0:.:73:0.0:0 +6 152332921 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:437,41:32.0:479:0.086:2 0:392,0:.:394:0.0:0 +6 152333032 rs117509702 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:75,12:32.0:87:0.138:2 0:52,0:.:52:0.0:0 +6 157150230 rs12206233 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:61,31:29.0:92:0.337 0:47,2:.:49:0.041 +6 157511319 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:375,15:30.0:391:0.038 0:374,2:.:376:0.005319 +6 159215375 rs983208 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,3:31.0:22:0.136:2 0:23,0:.:23:0.0:0 +6 160640117 . A G . PASS FAILURE_REASON=alt_allele_in_normal,clustered_read_position GT:AD:BQ:DP:FA 0/1:118,22:29.0:140:0.157 0:578,6:.:584:0.01 +6 161771037 rs62637702 T C . PASS DB;FAILURE_REASON=nearby_gap_events,alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:122,44:30.0:166:0.265 0:211,9:.:220:0.041 +6 161771039 . T C . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:127,48:31.0:176:0.274 0:228,0:.:229:0.0 +6 162137107 . C A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:785,72:30.0:857:0.084 0:801,2:.:804:0.002491 +6 162206873 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:429,64:31.0:494:0.13:2 0:534,0:.:534:0.0:0 +6 163528910 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:256,52:31.0:309:0.169:2 0:364,0:.:365:0.0:0 +6 169643879 rs73046003 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:78,38:31.0:116:0.328 0:46,2:.:48:0.042 +7 2166580 rs73037293 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:190,44:30.0:236:0.188:2 0:102,0:.:102:0.0:0 +7 2732378 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,3:31.0:22:0.136:2 0:11,0:.:11:0.0:0 +7 2951934 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:525,19:29.0:544:0.035:2 0:346,0:.:347:0.0:0 +7 2952915 rs199705831 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:512,17:29.0:529:0.032:2 0:231,0:.:231:0.0:0 +7 2962201 rs151225400 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:563,30:31.0:593:0.051:2 0:284,0:.:284:0.0:0 +7 2963744 rs190717725 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:182,12:32.0:194:0.062:2 0:53,0:.:53:0.0:0 +7 2968289 . T C . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:1127,20:30.0:1150:0.017 0:614,0:.:616:0.0 +7 2969660 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1092,55:29.0:1147:0.048:2 0:560,0:.:560:0.0:0 +7 2977768 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:148,7:30.0:156:0.045:2 0:90,0:.:90:0.0:0 +7 2985351 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:232,8:30.0:240:0.033:2 0:116,0:.:116:0.0:0 +7 6026530 rs1805324 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1169,68:29.0:1238:0.055:2 0:758,0:.:758:0.0:0 +7 6426892 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:756,35:31.0:792:0.044:2 0:517,1:.:519:0.001931:0 +7 6426908 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:680,56:31.0:737:0.076:2 0:494,0:.:495:0.0:0 +7 6438388 rs118039194 C T . PASS DB;FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:663,14:31.0:679:0.021 0:412,0:.:413:0.0 +7 6441993 rs61753123 C G . PASS DB;FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:621,15:31.0:637:0.024 0:477,0:.:479:0.0 +7 14026421 rs183005358 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:100,15:30.0:115:0.13:2 0:48,0:.:48:0.0:0 +7 14028575 rs187768235 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:550,74:30.0:625:0.119:2 0:384,0:.:384:0.0:0 +7 36859286 rs116070280 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:39,9:32.0:48:0.188:2 0:26,0:.:26:0.0:0 +7 39836727 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:124,12:30.0:136:0.088:2 0:45,0:.:45:0.0:0 +7 41729758 . C A . PASS FAILURE_REASON=possible_contamination,alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:1907,26:30.0:1935:0.013 0:1102,2:.:1105:0.001812 +7 41729759 . A G . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:1912,24:30.0:1937:0.012 0:1099,1:.:1102:0.0009091 +7 41730289 rs80087315 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:157,44:31.0:201:0.219:2 0:70,0:.:70:0.0:0 +7 43299616 rs9639872 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,16:33.0:35:0.457:2 0:43,0:.:43:0.0:0 +7 47092291 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:164,18:31.0:182:0.099:2 0:51,0:.:51:0.0:0 +7 50455179 . C A . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:368,7:31.0:375:0.019 0:217,0:.:218:0.0 +7 53854866 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:539,15:31.0:554:0.027:2 0:308,0:.:308:0.0:0 +7 55222593 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:566,19:30.0:586:0.032:2 0:249,0:.:250:0.0:0 +7 55228160 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:88,30:32.0:118:0.254:2 0:27,0:.:27:0.0:0 +7 56430693 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:51,4:31.0:55:0.073:2 0:23,0:.:23:0.0:0 +7 56430843 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:116,7:32.0:123:0.057:2 0:57,0:.:57:0.0:0 +7 56432708 rs116729273 T C . PASS DB;FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:4,67:33.0:71:0.944 0:27,11:.:38:0.289 +7 56432714 rs114688169 C A . PASS DB;FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:4,67:30.0:71:0.944 0:22,11:.:33:0.333 +7 57228283 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:23,4:29.0:27:0.148:2 0:17,0:.:17:0.0:0 +7 63230653 rs113079374 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:62,10:30.0:72:0.139:2 0:49,1:.:50:0.02:0 +7 65970787 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:586,31:31.0:617:0.05:2 0:494,0:.:494:0.0:0 +7 70859670 rs73700929 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:33,5:31.0:38:0.132:2 0:33,0:.:33:0.0:0 +7 81336535 rs5745745 C A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:263,97:30.0:360:0.269 0:224,12:.:236:0.051 +7 81340916 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:164,11:30.0:175:0.063:2 0:116,0:.:116:0.0:0 +7 81388001 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:731,46:29.0:779:0.059:2 0:573,1:.:574:0.001742:0 +7 92404285 rs3731302 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:45,6:32.0:52:0.118:2 0:20,0:.:20:0.0:0 +7 103275947 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:53,7:32.0:60:0.117:2 0:38,0:.:38:0.0:0 +7 106522693 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:359,144:31.0:503:0.286 0:357,3:.:362:0.008333 +7 116339672 rs35775721 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:415,14:29.0:429:0.033:2 0:380,0:.:380:0.0:0 +7 116397572 rs13223756 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:482,245:32.0:727:0.337 0:648,14:.:662:0.021 +7 116403127 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:340,10:30.0:350:0.029:2 0:284,0:.:284:0.0:0 +7 116411923 rs34589476 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:426,69:30.0:495:0.139:2 0:415,0:.:415:0.0:0 +7 116423161 rs2073560 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,8:29.0:27:0.296:2 0:19,0:.:19:0.0:0 +7 128766971 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:461,22:30.0:483:0.046:2 0:504,1:.:505:0.00198:0 +7 128767250 rs61740497 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:568,141:30.0:710:0.199:2 0:580,0:.:581:0.0:0 +7 128829066 rs41304185 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:42,5:33.0:47:0.106:2 0:66,0:.:67:0.0:0 +7 128845223 rs111482521 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:280,60:31.0:340:0.176:2 0:288,0:.:288:0.0:0 +7 128849078 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:404,55:30.0:459:0.12:2 0:424,0:.:424:0.0:0 +7 128850084 rs4728158 T G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:36,39:29.0:75:0.52:2 0:53,1:.:54:0.019:0 +7 128851674 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:240,11:32.0:251:0.044:2 0:180,0:.:181:0.0:0 +7 128852381 rs2075780 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:47,34:30.0:81:0.42:2 0:52,1:.:53:0.019:0 +7 135335822 rs73721607 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:108,32:30.0:140:0.229 0:116,3:.:119:0.025 +7 140453136 rs113488022 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:338,58:31.0:396:0.146:2 0:441,0:.:441:0.0:0 +7 140482427 rs1267642 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:322,152:32.0:474:0.321 0:372,12:.:384:0.031 +7 140483403 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:374,146:31.0:520:0.281:2 0:458,0:.:459:0.0:0 +7 140483605 rs1267644 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:319,128:30.0:447:0.286 0:376,14:.:392:0.036 +7 140486743 rs1270193 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:549,199:32.0:749:0.266 0:851,28:.:883:0.032 +7 140487494 rs117001169 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:540,98:29.0:639:0.154:2 0:584,0:.:585:0.0:0 +7 140488156 rs1267633 T G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:302,137:32.0:439:0.312 0:393,18:.:411:0.044 +7 140489173 rs145359047 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:910,46:32.0:956:0.048:2 0:936,0:.:937:0.0:0 +7 140492039 rs1267636 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:398,169:32.0:567:0.298 0:455,13:.:468:0.028 +7 140494413 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:440,69:32.0:509:0.136:2 0:544,0:.:544:0.0:0 +7 140496563 rs1639675 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:400,188:32.0:589:0.32 0:489,15:.:504:0.03 +7 140497586 rs73491871 A T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:342,164:31.0:506:0.324 0:384,17:.:401:0.042 +7 140507901 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:261,24:30.0:286:0.084:2 0:268,0:.:269:0.0:0 +7 151168756 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:347,84:30.0:432:0.195 0:328,2:.:331:0.006061 +7 151828793 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:32,10:31.0:42:0.238:2 0:34,0:.:34:0.0:0 +7 151836397 rs149140699 T C . PASS DB;FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:167,6:25.0:174:0.035 0:163,0:.:164:0.0 +7 151874581 rs149373512 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:418,91:32.0:510:0.179:2 0:500,0:.:500:0.0:0 +7 151875047 rs117187677 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:274,65:30.0:339:0.192 0:326,3:.:330:0.009119 +7 151891255 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:458,96:30.0:555:0.173:2 0:530,1:.:532:0.001883:0 +7 151946985 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:458,18:32.0:477:0.038:2 0:526,0:.:526:0.0:0 +7 151949735 rs77652527 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:388,226:32.0:614:0.368:2 0:574,0:.:577:0.0:0 +7 152373367 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:28,4:29.0:32:0.125:2 0:41,0:.:41:0.0:0 +7 153622478 rs113821224 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:344,25:30.0:369:0.068:2 0:277,0:.:278:0.0:0 +7 153622749 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:165,10:28.0:175:0.057:2 0:162,0:.:162:0.0:0 +7 154594008 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:108,9:30.0:117:0.077:2 0:85,0:.:85:0.0:0 +7 154594127 rs192817693 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:106,29:29.0:135:0.215:2 0:95,0:.:95:0.0:0 +7 155835626 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:230,9:32.0:239:0.038:2 0:154,0:.:155:0.0:0 +7 158451102 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:51,9:33.0:60:0.15:2 0:34,0:.:34:0.0:0 +8 2387994 rs17693045 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:88,30:30.0:118:0.254:2 0:185,0:.:185:0.0:0 +8 3489674 rs6996858 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:63,23:30.0:87:0.267 0:116,5:.:121:0.041 +8 3489677 rs6983641 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:63,25:31.0:88:0.284 0:121,5:.:126:0.04 +8 3489842 rs6998329 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:59,33:29.0:92:0.359 0:112,4:.:116:0.034 +8 5498584 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:18,3:29.0:21:0.143:2 0:10,0:.:10:0.0:0 +8 11096235 rs17153021 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:107,19:29.0:127:0.151 0:115,3:.:119:0.025 +8 11587234 rs11250159 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:89,42:31.0:131:0.321 0:218,7:.:226:0.031 +8 14166427 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,3:31.0:22:0.136:2 0:17,0:.:17:0.0:0 +8 14166825 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:248,132:30.0:380:0.347:2 0:561,0:.:562:0.0:0 +8 23548530 rs117285286 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:759,78:31.0:838:0.093:2 0:1096,0:.:1098:0.0:0 +8 29496868 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:118,16:31.0:134:0.119:2 0:122,0:.:122:0.0:0 +8 38279065 rs181303271 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:30,13:28.0:43:0.302:2 0:22,0:.:22:0.0:0 +8 38283759 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:331,37:30.0:370:0.101:2 0:459,0:.:459:0.0:0 +8 38297776 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:191,24:32.0:216:0.112:2 0:347,0:.:347:0.0:0 +8 55371474 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:37,5:29.0:42:0.119:2 0:34,0:.:34:0.0:0 +8 55374948 rs75598791 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:259,22:30.0:281:0.078:2 0:265,0:.:265:0.0:0 +8 59337497 . G C . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:150,74:32.0:224:0.33 0:140,0:.:140:0.0 +8 59339186 rs17261333 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:339,83:30.0:423:0.197:2 0:435,0:.:437:0.0:0 +8 70250559 rs183747339 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:25,5:30.0:30:0.167:2 0:25,0:.:25:0.0:0 +8 74885277 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:43,6:31.0:49:0.122:2 0:34,0:.:34:0.0:0 +8 90958341 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:279,23:29.0:302:0.076:2 0:257,0:.:257:0.0:0 +8 91434037 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:118,6:29.0:124:0.048:2 0:84,0:.:84:0.0:0 +8 109144106 . C T . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:31,5:28.0:36:0.139 0:25,0:.:25:0.0 +8 109735723 rs141694956 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:99,28:32.0:127:0.22 0:100,2:.:102:0.02 +8 117864369 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:568,80:31.0:648:0.123:2 0:378,0:.:379:0.0:0 +8 125875063 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:199,53:30.0:252:0.21:2 0:103,0:.:103:0.0:0 +8 128747953 rs3824120 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:253,41:31.0:294:0.139:2 0:153,0:.:153:0.0:0 +8 128751201 rs2070582 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:463,83:29.0:547:0.152 0:361,3:.:364:0.008242 +8 145736791 rs201586678 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:547,448:31.0:997:0.45:2 0:329,0:.:329:0.0:0 +8 145738441 rs200114521 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:517,528:30.0:1046:0.505:2 0:357,0:.:357:0.0:0 +9 1011900 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:13,3:31.0:16:0.188:2 0:11,0:.:11:0.0:0 +9 2039827 rs10964525 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:16,15:31.0:31:0.484:2 0:29,0:.:29:0.0:0 +9 5126742 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:356,39:31.0:395:0.099:2 0:441,0:.:441:0.0:0 +9 5456083 rs72705424 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:284,21:31.0:305:0.069:2 0:367,0:.:367:0.0:0 +9 8331548 rs76379489 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:399,32:31.0:431:0.074:2 0:507,0:.:507:0.0:0 +9 16206756 rs58804257 T G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:108,76:32.0:185:0.413 0:229,3:.:233:0.013 +9 20776854 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:78,24:31.0:102:0.235:2 0:100,0:.:100:0.0:0 +9 21993964 rs2811711 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:39,39:31.0:78:0.5:2 0:65,0:.:65:0.0:0 +9 22012051 rs13298881 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:233,122:32.0:355:0.344 0:399,24:.:423:0.057 +9 33676618 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:309,19:31.0:329:0.058:2 0:385,1:.:387:0.002591:0 +9 80646091 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=clustered_read_position GT:AD:BQ:DP:FA:SS 0/1:597,38:30.0:635:0.06:2 0:710,0:.:711:0.0:0 +9 80795416 rs60126017 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:67,37:33.0:104:0.356 0:114,12:.:126:0.095 +9 87570478 . C A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:411,61:31.0:473:0.129 0:487,2:.:490:0.00409 +9 93607915 rs114502181 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:279,49:30.0:328:0.149:2 0:255,0:.:256:0.0:0 +9 93636431 rs290228 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:322,233:32.0:555:0.42 0:510,31:.:542:0.057 +9 93641193 rs34231418 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:425,27:30.0:453:0.06:2 0:446,0:.:447:0.0:0 +9 93641199 rs2306040 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:276,156:32.0:432:0.361 0:410,20:.:431:0.047 +9 98009794 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:424,21:33.0:447:0.047:2 0:427,0:.:428:0.0:0 +9 98270324 rs28475503 A T . PASS DB;FAILURE_REASON=nearby_gap_events,possible_contamination GT:AD:BQ:DP:FA 0/1:91,5:24.0:96:0.052 0:90,0:.:91:0.0 +9 109484504 rs62567831 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:16,24:32.0:40:0.6:2 0:23,0:.:23:0.0:0 +9 133750550 rs35222907 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:80,39:32.0:120:0.328 0:115,2:.:117:0.017 +9 133759957 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:617,43:30.0:662:0.065:2 0:639,0:.:640:0.0:0 +9 135771515 rs116917669 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:50,39:29.0:89:0.438:2 0:56,1:.:57:0.018:0 +9 135782026 rs7870151 C A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:121,88:30.0:209:0.421 0:190,9:.:199:0.045 +9 135782221 rs7862221 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:213,182:32.0:395:0.461 0:322,24:.:346:0.069 +9 135786112 rs6597586 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:260,157:30.0:417:0.376 0:278,22:.:300:0.073 +9 135796608 rs17408598 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:40,28:31.0:68:0.412:2 0:46,1:.:47:0.021:0 +9 139391461 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:567,49:32.0:616:0.08:2 0:458,0:.:459:0.0:0 +9 139396113 rs11574906 T A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:100,84:29.0:184:0.457 0:90,7:.:97:0.072 +9 139397557 rs34383263 C G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:426,303:32.0:729:0.416 0:530,38:.:569:0.067 +9 139399641 rs13300218 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:104,76:30.0:180:0.422 0:89,5:.:94:0.053 +9 139401646 rs11574902 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:107,67:32.0:174:0.385 0:90,4:.:94:0.043 +9 139408892 rs3812609 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:11,128:29.0:139:0.921 0:56,3:.:59:0.051 +9 139412182 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:255,186:30.0:441:0.422:2 0:326,0:.:326:0.0:0 +9 139413908 rs2229975 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:407,293:30.0:701:0.419 0:505,2:.:507:0.003945 +9 139637329 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:35,4:32.0:39:0.103:2 0:47,0:.:47:0.0:0 +10 8100647 rs2229359 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:677,27:31.0:704:0.038:2 0:709,0:.:710:0.0:0 +10 8116079 rs2229360 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,40:30.0:59:0.678:2 0:28,0:.:28:0.0:0 +10 43596241 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:81,82:29.0:163:0.503:2 0:122,0:.:122:0.0:0 +10 43607471 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:112,12:31.0:124:0.097:2 0:87,0:.:87:0.0:0 +10 70406518 rs72799516 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:272,247:30.0:519:0.476:2 0:593,0:.:594:0.0:0 +10 70451383 rs183627556 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:636,102:28.0:739:0.138:2 0:920,0:.:920:0.0:0 +10 89692844 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:258,175:30.0:434:0.404:2 0:464,0:.:466:0.0:0 +10 123240645 rs3135821 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:331,292:30.0:624:0.469 0:629,48:.:678:0.071 +10 123241323 rs2912798 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:344,184:30.0:528:0.348 0:1098,51:.:1151:0.044 +10 123242589 rs2912797 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:168,125:30.0:293:0.427 0:284,16:.:300:0.053 +10 123274653 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:388,28:32.0:416:0.067:2 0:467,0:.:468:0.0:0 +11 2156741 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:656,100:32.0:756:0.132:2 0:691,0:.:691:0.0:0 +11 8248574 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:595,55:31.0:650:0.085:2 0:656,0:.:660:0.0:0 +11 17024886 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1,4:31.0:5:0.8:2 0:9,0:.:9:0.0:0 +11 17746976 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:829,33:30.0:862:0.038:2 0:810,0:.:810:0.0:0 +11 20575654 rs72938195 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:48,32:30.0:80:0.4:2 0:76,1:.:77:0.013:0 +11 21635295 rs56323531 T G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:139,72:31.0:212:0.341:2 0:198,0:.:198:0.0:0 +11 32437841 rs5030212 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,14:31.0:33:0.424:2 0:25,0:.:25:0.0:0 +11 32439001 rs5030198 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:67,40:31.0:107:0.374:2 0:85,0:.:85:0.0:0 +11 32452003 . A G . PASS FAILURE_REASON=nearby_gap_events,alt_allele_in_normal,clustered_read_position GT:AD:BQ:DP:FA 0/1:74,11:28.0:85:0.129 0:187,2:.:189:0.011 +11 39894274 rs11035553 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:72,41:31.0:113:0.363:2 0:126,0:.:126:0.0:0 +11 42138434 rs147928519 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:39,42:30.0:81:0.519:2 0:72,0:.:72:0.0:0 +11 64571710 . C T . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:371,6:29.0:377:0.016 0:339,0:.:339:0.0 +11 64575505 rs607969 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:559,67:31.0:627:0.107 0:676,2:.:681:0.00295 +11 69631013 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:292,37:30.0:330:0.112:2 0:205,0:.:206:0.0:0 +11 81185242 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:106,8:30.0:114:0.07:2 0:145,0:.:145:0.0:0 +11 85980945 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:62,5:32.0:67:0.075:2 0:52,0:.:52:0.0:0 +11 94203801 . C A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:303,27:31.0:330:0.082 0:335,2:.:337:0.005935 +11 94770943 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA:SS 0/1:422,35:28.0:458:0.077:2 0:325,0:.:325:0.0:0 +11 100999043 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1087,88:30.0:1177:0.075:2 0:855,0:.:856:0.0:0 +11 100999194 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1040,90:30.0:1132:0.08:2 0:881,0:.:882:0.0:0 +11 108115594 . C T . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:610,13:31.0:623:0.021 0:611,0:.:612:0.0 +11 108143456 rs1800057 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:547,229:31.0:778:0.295:2 0:634,1:.:635:0.001575:0 +11 108160632 rs184920614 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:26,30:30.0:56:0.536:2 0:46,1:.:47:0.021:0 +11 108225473 rs139490310 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:242,12:30.0:254:0.047:2 0:208,0:.:209:0.0:0 +11 118307774 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:43,4:26.0:47:0.085:2 0:20,0:.:20:0.0:0 +11 118342819 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:672,17:31.0:689:0.025:2 0:516,0:.:518:0.0:0 +11 118370615 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:379,11:32.0:391:0.028:2 0:363,0:.:363:0.0:0 +11 118372452 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:926,83:32.0:1012:0.082:2 0:960,0:.:962:0.0:0 +11 123606029 rs6590005 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:82,73:32.0:155:0.471 0:135,10:.:145:0.069 +12 401969 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1187,33:28.0:1221:0.027:2 0:786,0:.:786:0.0:0 +12 406427 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:236,28:30.0:264:0.106:2 0:121,0:.:121:0.0:0 +12 416764 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:876,68:30.0:944:0.072:2 0:582,0:.:582:0.0:0 +12 459805 . C A . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:1203,20:29.0:1223:0.016 0:731,0:.:732:0.0 +12 465673 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:781,72:33.0:853:0.084:2 0:635,0:.:636:0.0:0 +12 1022352 rs11571475 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:44,25:33.0:69:0.362 0:30,1:.:32:0.032 +12 1038854 rs11571424 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:140,25:31.0:165:0.152:2 0:48,0:.:48:0.0:0 +12 9848467 rs11052489 T A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:109,52:31.0:161:0.323 0:155,13:.:168:0.077 +12 12006544 rs17210957 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:670,136:31.0:808:0.169 0:717,2:.:720:0.002782 +12 12009741 rs2238126 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:953,200:32.0:1156:0.173:2 0:1002,0:.:1002:0.0:0 +12 12016089 rs2238131 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1258,97:31.0:1357:0.072:2 0:1336,0:.:1339:0.0:0 +12 12018392 rs76197219 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:904,179:31.0:1083:0.165:2 0:999,0:.:999:0.0:0 +12 12018911 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1320,74:31.0:1394:0.053:2 0:1138,0:.:1139:0.0:0 +12 12022533 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:578,364:30.0:943:0.386:2 0:814,0:.:816:0.0:0 +12 12029765 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:346,59:32.0:406:0.146:2 0:315,0:.:315:0.0:0 +12 12031265 rs150206595 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:244,45:30.0:289:0.156:2 0:290,0:.:290:0.0:0 +12 12873211 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:65,5:30.0:70:0.071:2 0:60,0:.:60:0.0:0 +12 13767996 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:9,3:30.0:12:0.25:2 0:11,0:.:11:0.0:0 +12 16753747 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:117,21:29.0:138:0.152:2 0:91,0:.:92:0.0:0 +12 18467122 rs143458306 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:37,66:32.0:103:0.641:2 0:51,0:.:51:0.0:0 +12 18524061 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:291,18:32.0:309:0.058:2 0:239,0:.:239:0.0:0 +12 18690977 rs11044171 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:41,13:28.0:54:0.241:2 0:53,0:.:53:0.0:0 +12 18715728 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:370,31:32.0:402:0.077:2 0:659,0:.:660:0.0:0 +12 21600952 rs11046061 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:23,8:26.0:31:0.258:2 0:59,1:.:61:0.017:0 +12 25398285 rs121913530 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:649,82:30.0:731:0.112:2 0:461,0:.:461:0.0:0 +12 27578740 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:12,13:28.0:25:0.52:2 0:11,0:.:11:0.0:0 +12 38601111 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:28,7:26.0:35:0.2:2 0:24,0:.:24:0.0:0 +12 43131208 rs10506217 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:10,22:31.0:32:0.688:2 0:37,1:.:38:0.026:0 +12 46254505 rs183616884 C G . PASS DB;FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:102,11:32.0:113:0.097 0:159,0:.:160:0.0 +12 46287550 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:96,11:29.0:107:0.103:2 0:163,0:.:163:0.0:0 +12 49428717 rs148688181 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:536,45:30.0:581:0.077:2 0:436,1:.:437:0.002288:0 +12 49431654 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:584,110:30.0:694:0.159:2 0:493,0:.:495:0.0:0 +12 49436248 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:250,45:29.0:295:0.153:2 0:208,0:.:208:0.0:0 +12 49438490 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:334,145:30.0:479:0.303:2 0:406,0:.:406:0.0:0 +12 50413034 rs76465602 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:133,8:32.0:141:0.057:2 0:142,1:.:143:0.006993:0 +12 50484405 rs79510657 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:224,59:31.0:283:0.208:2 0:258,0:.:259:0.0:0 +12 52906545 rs79750494 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:57,4:30.0:62:0.066:2 0:49,0:.:49:0.0:0 +12 52921297 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:279,24:30.0:303:0.079:2 0:180,0:.:180:0.0:0 +12 53030489 rs73109357 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:65,11:31.0:76:0.145:2 0:61,0:.:61:0.0:0 +12 55427158 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:95,7:31.0:102:0.069:2 0:56,0:.:56:0.0:0 +12 56489613 rs138072655 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:253,75:32.0:328:0.229:2 0:316,0:.:316:0.0:0 +12 57860293 rs182191937 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:146,10:32.0:156:0.064:2 0:94,0:.:94:0.0:0 +12 57865284 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1130,70:30.0:1201:0.058:2 0:1100,0:.:1101:0.0:0 +12 58144359 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:146,78:29.0:224:0.348:2 0:160,0:.:161:0.0:0 +12 61873046 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:225,11:31.0:236:0.047:2 0:224,0:.:224:0.0:0 +12 69202867 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:120,13:30.0:133:0.098:2 0:74,0:.:74:0.0:0 +12 77054235 rs12817158 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:40,53:30.0:93:0.57 0:80,3:.:83:0.036 +12 87756834 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:3,3:31.0:6:0.5:2 0:11,0:.:11:0.0:0 +12 91238015 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:46,15:30.0:61:0.246:2 0:67,0:.:67:0.0:0 +12 97487834 . T G . PASS FAILURE_REASON=nearby_gap_events,possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:301,8:29.0:309:0.026 0:344,1:.:345:0.002899 +12 115109672 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:564,28:28.0:592:0.047:2 0:601,1:.:602:0.001661:0 +12 115110078 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:295,11:30.0:306:0.036:2 0:253,0:.:253:0.0:0 +12 115112315 . G T . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:75,14:31.0:89:0.157 0:70,2:.:72:0.028 +12 115117337 rs34627348 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:543,113:30.0:656:0.172:2 0:733,0:.:733:0.0:0 +12 115118589 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:163,29:31.0:192:0.151:2 0:172,0:.:172:0.0:0 +12 120541570 rs17499109 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:510,154:29.0:664:0.232:2 0:441,1:.:442:0.002262:0 +12 120541597 rs73217390 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:710,206:29.0:917:0.225 0:671,2:.:673:0.002972 +12 120554466 rs191322615 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:238,183:30.0:421:0.435:2 0:319,1:.:321:0.003125:0 +12 121435778 rs56097722 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:53,7:27.0:60:0.117:2 0:41,0:.:41:0.0:0 +12 132001302 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:5,3:29.0:8:0.375:2 0:10,0:.:10:0.0:0 +12 132001303 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:5,3:27.0:8:0.375:2 0:10,0:.:10:0.0:0 +12 133208752 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:41,5:30.0:46:0.109:2 0:32,0:.:32:0.0:0 +12 133211059 rs5745004 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:61,31:31.0:92:0.337:2 0:70,0:.:70:0.0:0 +12 133257837 rs34047482 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:345,21:30.0:368:0.057:2 0:436,1:.:438:0.002288:0 +13 21004758 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:216,11:31.0:227:0.048:2 0:239,0:.:239:0.0:0 +13 28611186 rs17086239 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:25,20:31.0:45:0.444:2 0:47,1:.:48:0.021:0 +13 28611221 rs17086242 T C . PASS DB;FAILURE_REASON=nearby_gap_events,alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:45,31:31.0:76:0.408 0:82,3:.:86:0.035 +13 28644610 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:275,27:33.0:302:0.089:2 0:348,0:.:348:0.0:0 +13 28964198 rs17537350 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:365,13:31.0:378:0.034:2 0:402,1:.:403:0.002481:0 +13 28971220 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:165,64:30.0:229:0.279 0:220,2:.:223:0.009009 +13 32747212 rs17077178 C G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:59,45:31.0:104:0.433 0:116,4:.:120:0.033 +13 32899388 rs11571610 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:51,46:30.0:97:0.474 0:140,8:.:148:0.054 +13 32906480 rs766173 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:297,202:32.0:499:0.405 0:476,27:.:504:0.054 +13 32906980 rs1801439 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:153,98:30.0:251:0.39 0:247,15:.:262:0.057 +13 32910351 rs11571651 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:178,156:30.0:334:0.467 0:330,27:.:357:0.076 +13 32910721 rs1801499 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:683,489:32.0:1173:0.417 0:1172,90:.:1263:0.071 +13 32911463 rs1799944 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:630,521:31.0:1151:0.453 0:1174,81:.:1255:0.065 +13 32929478 rs11147489 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:422,423:31.0:847:0.501 0:910,63:.:976:0.065 +13 32930673 rs28897744 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:317,104:30.0:421:0.247:2 0:473,1:.:474:0.00211:0 +13 32968793 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:144,14:33.0:158:0.089:2 0:171,0:.:171:0.0:0 +13 41032432 rs17258297 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:85,44:31.0:130:0.341:2 0:130,0:.:131:0.0:0 +13 41161979 rs2984121 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:722,51:32.0:773:0.066:2 0:790,0:.:790:0.0:0 +13 49037825 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:218,27:30.0:245:0.11:2 0:232,1:.:233:0.004292:0 +13 49047529 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:172,113:32.0:286:0.396:2 0:338,0:.:339:0.0:0 +13 67591561 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:70,31:31.0:101:0.307:2 0:64,0:.:64:0.0:0 +13 67591562 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:73,30:32.0:103:0.291:2 0:65,0:.:65:0.0:0 +13 68406205 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:44,10:27.0:54:0.185:2 0:52,0:.:52:0.0:0 +13 73348372 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:16,3:33.0:19:0.158:2 0:11,0:.:11:0.0:0 +13 103504331 rs41548912 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:47,4:30.0:51:0.078:2 0:34,0:.:34:0.0:0 +13 103508378 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:189,36:30.0:225:0.16:2 0:235,1:.:236:0.004237:0 +13 106826430 rs1887896 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:154,48:30.0:202:0.238 0:222,6:.:228:0.026 +13 110428923 rs9559654 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:50,159:28.0:209:0.761 0:155,7:.:162:0.043 +13 110435914 rs12853546 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:43,136:30.0:179:0.76 0:130,3:.:133:0.023 +14 20893115 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:275,19:31.0:294:0.065:2 0:154,0:.:154:0.0:0 +14 23652305 rs73600433 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:621,390:31.0:1011:0.386 0:804,37:.:841:0.044 +14 23764770 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:68,20:32.0:88:0.227:2 0:48,0:.:48:0.0:0 +14 25438196 rs78425257 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:318,29:31.0:347:0.084:2 0:180,0:.:180:0.0:0 +14 35872920 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:3872,168:30.0:4042:0.042:2 0:1249,0:.:1249:0.0:0 +14 36988175 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:218,1008:30.0:1227:0.822:2 0:150,0:.:150:0.0:0 +14 38060768 rs35342092 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:5080,126:31.0:5207:0.024 0:1372,3:.:1377:0.002182 +14 38061106 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:626,24:30.0:651:0.037:2 0:128,0:.:128:0.0:0 +14 48351664 rs61993497 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:202,33:33.0:235:0.14 0:177,5:.:182:0.027 +14 61799788 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:287,42:31.0:329:0.128:2 0:248,0:.:248:0.0:0 +14 65544815 rs184998980 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:125,67:29.0:192:0.349:2 0:103,0:.:103:0.0:0 +14 65568285 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:291,20:31.0:311:0.064:2 0:297,0:.:299:0.0:0 +14 69061259 rs28908468 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:151,76:31.0:227:0.335:2 0:141,0:.:141:0.0:0 +14 69117298 rs79769103 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:48,7:30.0:55:0.127:2 0:28,0:.:28:0.0:0 +14 69117450 rs74506607 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:490,67:32.0:557:0.12:2 0:385,0:.:385:0.0:0 +14 70439711 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:13,3:31.0:16:0.188:2 0:8,0:.:8:0.0:0 +14 77493815 rs7156498 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:26,3:32.0:29:0.103:2 0:54,0:.:54:0.0:0 +14 80471852 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:255,43:31.0:298:0.144:2 0:221,0:.:221:0.0:0 +14 81563195 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:83,20:31.0:103:0.194:2 0:25,0:.:25:0.0:0 +14 87813148 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:111,6:32.0:117:0.051:2 0:69,0:.:69:0.0:0 +14 87813214 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:37,7:31.0:44:0.159:2 0:20,0:.:20:0.0:0 +14 88360375 rs35362358 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:13,10:30.0:23:0.435:2 0:20,0:.:20:0.0:0 +14 95556644 . A C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:22,6:32.0:28:0.214:2 0:11,0:.:11:0.0:0 +14 95560444 rs139500905 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:345,24:29.0:369:0.065:2 0:278,0:.:278:0.0:0 +14 95562999 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:693,60:29.0:754:0.08:2 0:532,0:.:533:0.0:0 +14 95591070 rs67737119 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:47,32:31.0:79:0.405:2 0:45,0:.:45:0.0:0 +14 103707780 rs17101400 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:25,9:31.0:34:0.265 0:30,1:.:31:0.032 +14 105238820 rs61761201 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:451,37:32.0:489:0.076:2 0:254,0:.:255:0.0:0 +14 105241103 . C G . PASS FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:69,4:31.0:73:0.055 0:16,0:.:16:0.0 +14 105241378 rs3730346 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:870,305:31.0:1176:0.26 0:548,13:.:565:0.023 +14 105241607 rs182149357 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:292,109:31.0:401:0.272:2 0:183,0:.:184:0.0:0 +15 26216159 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:21,3:32.0:24:0.125:2 0:10,0:.:10:0.0:0 +15 35385071 rs28629832 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:322,218:31.0:542:0.404 0:538,26:.:565:0.046 +15 42046575 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:240,10:30.0:250:0.04:2 0:199,0:.:199:0.0:0 +15 59845326 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:7,4:29.0:11:0.364:2 0:11,0:.:11:0.0:0 +15 64281668 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:7,4:32.0:11:0.364:2 0:12,0:.:12:0.0:0 +15 66679684 rs77796976 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:653,52:32.0:705:0.074:2 0:766,0:.:766:0.0:0 +15 66779698 rs41315964 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:156,43:30.0:200:0.216:2 0:204,0:.:205:0.0:0 +15 66782048 rs41306345 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:387,81:30.0:468:0.173:2 0:554,0:.:554:0.0:0 +15 67473790 rs117185005 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:260,181:30.0:441:0.41:2 0:397,0:.:400:0.0:0 +15 88126117 rs118139016 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:143,94:29.0:238:0.397:2 0:262,1:.:264:0.003802:0 +15 88472228 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:35,6:31.0:41:0.146:2 0:17,0:.:17:0.0:0 +15 88472655 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:240,161:30.0:401:0.401:2 0:286,0:.:287:0.0:0 +15 91292969 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:372,19:30.0:391:0.049:2 0:401,0:.:402:0.0:0 +15 92829452 rs28566962 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:96,77:30.0:173:0.445 0:124,8:.:132:0.061 +15 99460184 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:112,34:30.0:146:0.233:2 0:117,0:.:117:0.0:0 +15 99467930 rs186895929 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:322,78:30.0:401:0.195:2 0:317,1:.:318:0.003145:0 +15 99861641 rs149886786 T G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:250,52:31.0:302:0.172:2 0:315,0:.:315:0.0:0 +16 339415 rs387467 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:360,168:30.0:531:0.318 0:323,16:.:339:0.047 +16 339727 rs423749 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:63,29:27.0:92:0.315:2 0:43,0:.:43:0.0:0 +16 347184 rs214252 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:517,191:30.0:708:0.27 0:549,16:.:567:0.028 +16 347326 rs214251 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:72,36:30.0:108:0.333:2 0:43,0:.:43:0.0:0 +16 360149 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:195,9:30.0:204:0.044:2 0:118,0:.:118:0.0:0 +16 396234 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:595,22:30.0:617:0.036:2 0:513,0:.:513:0.0:0 +16 1987179 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:31,7:30.0:38:0.184:2 0:30,0:.:30:0.0:0 +16 2110795 rs1800725 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:510,125:31.0:635:0.197:2 0:471,1:.:472:0.002119:0 +16 2132583 rs1800705 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:140,81:30.0:222:0.367:2 0:126,0:.:127:0.0:0 +16 2134852 rs148656621 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:217,109:30.0:326:0.334:2 0:156,0:.:157:0.0:0 +16 2136455 rs76029733 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:173,36:29.0:209:0.172:2 0:107,0:.:107:0.0:0 +16 2215659 . C G . PASS FAILURE_REASON=clustered_read_position GT:AD:BQ:DP:FA 0/1:58,8:27.0:66:0.121 0:18,0:.:18:0.0 +16 2215660 . T C . PASS FAILURE_REASON=clustered_read_position GT:AD:BQ:DP:FA 0/1:57,10:30.0:67:0.149 0:20,0:.:20:0.0 +16 2226763 rs184220090 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:58,7:32.0:65:0.108:2 0:21,0:.:21:0.0:0 +16 3786594 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:351,44:31.0:396:0.111:2 0:305,0:.:305:0.0:0 +16 3794705 rs129972 T G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:53,14:30.0:67:0.209:2 0:41,0:.:41:0.0:0 +16 3807171 rs140586932 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:28,16:30.0:44:0.364:2 0:58,0:.:59:0.0:0 +16 3807946 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:402,33:30.0:435:0.076:2 0:472,0:.:472:0.0:0 +16 3860554 rs190677981 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:201,103:31.0:304:0.339:2 0:243,0:.:243:0.0:0 +16 10273821 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:269,18:31.0:287:0.063:2 0:208,0:.:208:0.0:0 +16 10353357 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:9,3:31.0:12:0.25:2 0:13,0:.:13:0.0:0 +16 14028861 rs3136150 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:32,7:31.0:39:0.179:2 0:28,0:.:28:0.0:0 +16 14041760 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:513,16:29.0:529:0.03:2 0:568,0:.:568:0.0:0 +16 14042077 rs1800124 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:439,45:32.0:484:0.093:2 0:502,0:.:502:0.0:0 +16 27356584 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:83,47:32.0:130:0.362:2 0:108,0:.:108:0.0:0 +16 30129936 rs12922100 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:152,86:30.0:238:0.361:2 0:197,1:.:198:0.005051:0 +16 33373312 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:463,22:29.0:485:0.045:2 0:911,0:.:911:0.0:0 +16 56866196 rs2241770 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:658,159:31.0:817:0.195 0:812,27:.:840:0.032 +16 56871762 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:72,15:32.0:87:0.172:2 0:56,0:.:56:0.0:0 +16 56872824 rs3764266 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:432,128:29.0:560:0.229 0:541,25:.:566:0.044 +16 58960831 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:40,24:29.0:64:0.375:2 0:44,0:.:44:0.0:0 +16 68862182 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:343,13:32.0:357:0.037:2 0:423,0:.:423:0.0:0 +16 72822296 rs2228199 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:1075,240:31.0:1317:0.183 0:1381,51:.:1433:0.036 +16 72828383 . C T . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:820,207:30.0:1029:0.202 0:1009,3:.:1013:0.002964 +16 72830539 rs62051555 C G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:1106,215:32.0:1323:0.163 0:1311,41:.:1355:0.03 +16 72832377 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:1072,49:31.0:1121:0.044 0:1065,3:.:1070:0.002809 +16 72991718 . G A . PASS FAILURE_REASON=nearby_gap_events,possible_contamination GT:AD:BQ:DP:FA 0/1:681,7:29.0:688:0.01 0:590,1:.:592:0.001692 +16 72993622 rs62053190 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:805,143:31.0:949:0.151 0:964,27:.:996:0.027 +16 72993706 rs62053191 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:834,150:30.0:984:0.152 0:981,25:.:1006:0.025 +16 81887977 rs34028338 G C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:149,82:31.0:231:0.355 0:207,7:.:214:0.033 +16 81888274 rs41305759 C A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:143,97:30.0:240:0.404 0:223,11:.:234:0.047 +16 81891790 rs36114479 C G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:186,82:32.0:268:0.306 0:230,7:.:237:0.03 +16 81892645 rs150054348 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:111,25:31.0:136:0.184:2 0:123,0:.:123:0.0:0 +16 81892646 rs185238046 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:119,22:30.0:141:0.156:2 0:131,0:.:131:0.0:0 +16 81892913 rs12596639 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:91,37:31.0:128:0.289 0:98,4:.:102:0.039 +16 81917099 rs6564928 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:66,26:30.0:92:0.283 0:65,3:.:68:0.044 +16 81946328 rs138158454 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:603,316:29.0:920:0.344 0:803,3:.:807:0.003722 +16 81957227 rs4485361 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:469,101:30.0:570:0.177:2 0:552,0:.:552:0.0:0 +16 81957349 rs117954043 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:85,13:29.0:98:0.133:2 0:43,0:.:43:0.0:0 +16 81990505 rs45491692 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:465,238:30.0:705:0.339:2 0:701,0:.:704:0.0:0 +16 89350597 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1331,164:32.0:1496:0.11:2 0:1549,0:.:1550:0.0:0 +16 89357823 . C G . PASS FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:39,3:30.0:42:0.071 0:9,0:.:9:0.0 +16 89839915 rs117477270 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:72,6:31.0:79:0.077:2 0:65,0:.:65:0.0:0 +17 3568401 rs3817666 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:16,8:30.0:24:0.333:2 0:22,0:.:22:0.0:0 +17 4540268 rs11568145 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:127,11:32.0:139:0.08:2 0:147,0:.:147:0.0:0 +17 7577407 rs12951053 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:49,67:32.0:116:0.578 0:139,6:.:146:0.041 +17 7577427 rs12947788 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:59,84:30.0:143:0.587 0:184,8:.:195:0.042 +17 7578461 rs121912654 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:206,108:30.0:314:0.344:2 0:436,0:.:438:0.0:0 +17 7580500 rs12944939 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:30,65:31.0:95:0.684 0:95,3:.:98:0.031 +17 7976917 rs78835850 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:161,69:29.0:230:0.3:2 0:208,0:.:209:0.0:0 +17 7983681 rs2304906 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:269,32:30.0:301:0.106:2 0:273,0:.:273:0.0:0 +17 7984157 rs3816263 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:398,119:31.0:517:0.23 0:423,16:.:439:0.036 +17 15983458 rs118072442 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:118,75:30.0:193:0.389:2 0:176,0:.:176:0.0:0 +17 16049563 rs183071464 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=clustered_read_position GT:AD:BQ:DP:FA:SS 0/1:88,11:30.0:99:0.111:2 0:87,1:.:88:0.011:0 +17 21544599 rs9912297 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:251,121:31.0:372:0.325 0:318,14:.:332:0.042 +17 29585907 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:38,8:30.0:46:0.174:2 0:13,0:.:13:0.0:0 +17 29587341 rs17881285 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:264,51:30.0:315:0.162:2 0:306,0:.:306:0.0:0 +17 30315470 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:556,129:30.0:686:0.188:2 0:747,0:.:748:0.0:0 +17 33430327 . C A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:666,69:30.0:736:0.094 0:689,3:.:693:0.004335 +17 37618220 rs192819848 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:87,14:31.0:101:0.139:2 0:57,0:.:57:0.0:0 +17 37646947 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:621,25:29.0:646:0.039:2 0:595,0:.:595:0.0:0 +17 37866797 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:171,31:27.0:204:0.153:2 0:128,0:.:128:0.0:0 +17 37871848 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:307,44:30.0:351:0.125:2 0:201,0:.:201:0.0:0 +17 38497450 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:78,9:30.0:87:0.103:2 0:20,0:.:20:0.0:0 +17 38497833 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:443,22:30.0:465:0.047:2 0:384,1:.:385:0.002597:0 +17 38497884 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:393,67:30.0:461:0.146:2 0:407,1:.:408:0.002451:0 +17 38512197 rs8069541 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:172,124:31.0:296:0.419 0:168,11:.:179:0.061 +17 38512457 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:787,30:31.0:818:0.037:2 0:572,0:.:574:0.0:0 +17 38512461 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:779,30:30.0:811:0.037:2 0:575,1:.:579:0.001736:0 +17 40467934 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:349,12:30.0:361:0.033:2 0:205,0:.:205:0.0:0 +17 40489660 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:617,32:30.0:651:0.049:2 0:546,0:.:548:0.0:0 +17 41244880 rs80357200 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:441,45:31.0:487:0.093:2 0:384,0:.:385:0.0:0 +17 41267608 . G C . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:153,6:32.0:160:0.038 0:121,0:.:121:0.0 +17 43344458 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:436,21:30.0:457:0.046:2 0:364,0:.:364:0.0:0 +17 43352049 rs17685379 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:29,256:28.0:285:0.898 0:111,9:.:120:0.075 +17 46801231 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:193,10:29.0:203:0.049:2 0:107,0:.:107:0.0:0 +17 46802314 rs116931900 G T . PASS DB;FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:52,4:30.0:56:0.071 0:27,0:.:27:0.0 +17 54445637 rs71137202 C G . PASS DB;FAILURE_REASON=clustered_read_position GT:AD:BQ:DP:FA 0/1:79,13:31.0:92:0.141 0:86,0:.:90:0.0 +17 56440474 rs2632517 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:132,26:30.0:158:0.165:2 0:60,0:.:60:0.0:0 +17 56440642 rs76384648 C T . PASS DB;FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:1157,52:30.0:1209:0.043 0:823,0:.:825:0.0 +17 56811731 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:44,4:31.0:48:0.083:2 0:29,0:.:29:0.0:0 +17 58678009 . T A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:517,105:31.0:624:0.169:2 0:538,1:.:540:0.001855:0 +17 59924512 rs4988346 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:863,40:29.0:905:0.044:2 0:720,0:.:720:0.0:0 +17 59926645 rs4988343 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:160,114:28.0:274:0.416:2 0:163,0:.:163:0.0:0 +17 61307713 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:12,3:33.0:15:0.2:2 0:10,0:.:10:0.0:0 +17 62008760 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:491,216:30.0:708:0.306:2 0:474,0:.:474:0.0:0 +17 70120111 rs929651 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:173,18:31.0:191:0.094:2 0:66,0:.:66:0.0:0 +17 77280452 rs117415787 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:24,36:32.0:60:0.6:2 0:26,0:.:26:0.0:0 +17 78796907 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:500,27:32.0:530:0.051:2 0:422,0:.:423:0.0:0 +17 78829114 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:87,5:33.0:92:0.054:2 0:52,0:.:52:0.0:0 +17 78857631 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:612,33:30.0:645:0.051:2 0:437,0:.:437:0.0:0 +17 78919466 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:783,27:31.0:810:0.033:2 0:617,0:.:618:0.0:0 +17 78934088 rs77734083 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:91,66:32.0:157:0.42:2 0:86,0:.:86:0.0:0 +18 8413657 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:476,30:30.0:506:0.059:2 0:376,0:.:376:0.0:0 +18 12912750 rs74405000 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:95,7:30.0:102:0.069:2 0:81,0:.:81:0.0:0 +18 12912821 rs74870438 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:329,19:31.0:348:0.055:2 0:314,0:.:314:0.0:0 +18 18517151 . A C . PASS FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:4,3:31.0:7:0.429 0:47,5:.:52:0.096 +18 28787634 rs78796387 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:40,9:30.0:49:0.184:2 0:51,1:.:52:0.019:0 +18 39537688 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:212,166:32.0:378:0.439:2 0:434,0:.:434:0.0:0 +18 48190817 rs45471400 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:68,64:29.0:132:0.485 0:148,12:.:160:0.075 +19 1221161 rs9282860 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:301,156:30.0:457:0.341 0:398,20:.:418:0.048 +19 1611856 rs62130064 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:674,37:30.0:711:0.052:2 0:744,1:.:745:0.001342:0 +19 1622115 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:813,25:31.0:838:0.03:2 0:649,0:.:651:0.0:0 +19 2211220 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:405,17:31.0:424:0.04:2 0:382,0:.:382:0.0:0 +19 2217203 rs72985483 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:52,7:30.0:59:0.119:2 0:33,0:.:33:0.0:0 +19 3110361 rs41276846 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:171,72:30.0:243:0.296 0:242,8:.:251:0.032 +19 3114864 rs3746069 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:120,42:31.0:163:0.259 0:119,5:.:124:0.04 +19 3118851 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:214,18:29.0:232:0.078:2 0:129,0:.:129:0.0:0 +19 4102449 rs17851657 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:166,280:31.0:446:0.628 0:427,31:.:458:0.068 +19 5174304 rs76272020 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:22,9:28.0:31:0.29:2 0:20,0:.:20:0.0:0 +19 5206724 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:186,84:30.0:270:0.311:2 0:240,0:.:240:0.0:0 +19 5208216 rs60630722 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:187,198:30.0:385:0.514 0:313,24:.:337:0.071 +19 5208257 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:555,37:30.0:592:0.063:2 0:556,0:.:556:0.0:0 +19 5212482 rs2230611 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:216,302:30.0:518:0.583 0:490,21:.:511:0.041 +19 5212586 rs4807696 G T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:73,82:30.0:155:0.529 0:105,6:.:111:0.054 +19 5218684 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:189,80:31.0:269:0.297:2 0:170,0:.:170:0.0:0 +19 5222088 rs3746131 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:107,113:32.0:220:0.514:2 0:188,0:.:188:0.0:0 +19 5229728 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:10,5:30.0:15:0.333:2 0:15,0:.:15:0.0:0 +19 5240392 rs3746130 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:139,95:29.0:234:0.406 0:193,8:.:201:0.04 +19 7123031 rs148813626 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:247,146:30.0:395:0.372 0:358,14:.:372:0.038 +19 7132343 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:133,67:31.0:200:0.335:2 0:198,0:.:198:0.0:0 +19 7162968 . C T . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:149,5:32.0:154:0.032 0:160,0:.:160:0.0 +19 7172526 rs41412545 C A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:40,26:31.0:66:0.394:2 0:66,0:.:66:0.0:0 +19 7184238 rs6510959 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:71,76:28.0:147:0.517 0:148,11:.:160:0.069 +19 7184243 rs41315074 C G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:80,79:32.0:159:0.497 0:173,8:.:181:0.044 +19 7184490 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:240,133:31.0:374:0.357 0:471,2:.:473:0.004228 +19 7805951 rs11465413 A T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:45,711:31.0:756:0.94 0:780,53:.:833:0.064 +19 7815690 rs111296792 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:36,13:31.0:49:0.265:2 0:45,0:.:45:0.0:0 +19 10260400 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:142,7:30.0:149:0.047:2 0:137,0:.:137:0.0:0 +19 10278953 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:284,74:32.0:358:0.207:2 0:407,0:.:408:0.0:0 +19 10292608 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:71,7:27.0:78:0.09:2 0:82,0:.:82:0.0:0 +19 10292901 rs78789647 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:33,7:30.0:40:0.175:2 0:33,1:.:34:0.029:0 +19 10610017 rs12985702 G C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:131,94:30.0:225:0.418 0:228,10:.:238:0.042 +19 11130431 rs45565139 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:231,92:31.0:323:0.285:2 0:361,1:.:362:0.002762:0 +19 11169305 rs36049922 T C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:47,28:32.0:75:0.373 0:39,2:.:42:0.049 +19 13051554 rs184881678 G T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:695,319:30.0:1014:0.315:2 0:979,0:.:984:0.0:0 +19 14627140 rs45454593 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:792,338:30.0:1132:0.299:2 0:1274,1:.:1276:0.0007843:0 +19 14629336 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:23,11:31.0:34:0.324:2 0:20,0:.:20:0.0:0 +19 15291576 rs35769976 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:423,210:32.0:633:0.332:2 0:532,0:.:534:0.0:0 +19 15291699 rs57538005 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:233,97:31.0:330:0.294:2 0:220,0:.:222:0.0:0 +19 15296513 rs147014533 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:276,115:28.0:392:0.294:2 0:320,0:.:321:0.0:0 +19 15299048 rs114207045 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:392,188:30.0:580:0.324:2 0:494,0:.:494:0.0:0 +19 15308287 rs188132716 G C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:390,171:30.0:561:0.305 0:487,2:.:489:0.00409 +19 15890626 rs55782900 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:37,58:31.0:95:0.611:2 0:73,1:.:74:0.014:0 +19 17953950 rs55778349 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:395,27:30.0:422:0.064:2 0:407,1:.:409:0.002451:0 +19 18271576 rs11670635 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:49,17:30.0:66:0.258:2 0:44,0:.:44:0.0:0 +19 18277820 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:90,11:32.0:101:0.109:2 0:73,0:.:73:0.0:0 +19 18279861 . C T . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:268,6:31.0:275:0.022 0:219,0:.:219:0.0 +19 18280096 rs149081991 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:37,19:29.0:56:0.339 0:58,2:.:60:0.033 +19 19260105 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:494,21:31.0:515:0.041:2 0:444,0:.:444:0.0:0 +19 30311555 rs201798088 C T . PASS DB;FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:193,14:29.0:207:0.068 0:130,2:.:132:0.015 +19 30312874 rs3218066 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:381,238:30.0:619:0.384:2 0:475,0:.:475:0.0:0 +19 30313622 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:78,9:29.0:87:0.103:2 0:60,0:.:60:0.0:0 +19 33905969 rs77619050 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:25,9:30.0:34:0.265:2 0:19,0:.:19:0.0:0 +19 34080443 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:52,32:31.0:84:0.381:2 0:54,0:.:54:0.0:0 +19 34080444 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:52,32:30.0:84:0.381:2 0:53,0:.:53:0.0:0 +19 39538680 rs116959993 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:95,17:30.0:112:0.152:2 0:82,0:.:82:0.0:0 +19 41727143 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:512,117:31.0:629:0.186:2 0:501,0:.:506:0.0:0 +19 41727197 rs2271546 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:255,76:30.0:331:0.23:2 0:221,0:.:221:0.0:0 +19 41749397 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:221,17:30.0:238:0.071:2 0:142,0:.:142:0.0:0 +19 41759474 rs73045223 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:480,41:30.0:521:0.079:2 0:375,0:.:375:0.0:0 +19 41763269 rs141726434 A T . PASS DB;FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:152,5:31.0:157:0.032 0:100,0:.:100:0.0 +19 42384572 rs141689896 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:131,8:29.0:139:0.058:2 0:64,1:.:65:0.015:0 +19 42790821 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:310,13:31.0:324:0.04:2 0:215,1:.:217:0.00463:0 +19 42791015 . C A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:822,41:30.0:863:0.048 0:560,2:.:563:0.003559 +19 42795554 rs10410185 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:832,146:30.0:979:0.149:2 0:710,1:.:713:0.001406:0 +19 42797603 rs78756053 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:92,15:31.0:107:0.14:2 0:30,0:.:30:0.0:0 +19 45856260 rs185386615 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:289,21:30.0:310:0.068:2 0:209,0:.:209:0.0:0 +19 50906507 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:499,53:30.0:552:0.096:2 0:476,1:.:478:0.002096:0 +19 50910196 rs3219396 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:537,65:28.0:604:0.108 0:568,2:.:576:0.003509 +19 50912821 rs144143245 G C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:773,98:31.0:871:0.113:2 0:762,0:.:766:0.0:0 +19 50916796 . G A . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:565,6:30.0:571:0.011 0:535,1:.:536:0.001866 +19 52693297 rs111861947 C T . PASS DB;FAILURE_REASON=nearby_gap_events,possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:150,6:30.0:156:0.038 0:136,0:.:136:0.0 +20 1421974 rs35310517 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:140,26:33.0:166:0.157:2 0:110,0:.:110:0.0:0 +20 30296422 rs73117925 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:196,100:31.0:297:0.338:2 0:206,0:.:206:0.0:0 +20 30296428 rs117532975 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:263,68:30.0:331:0.205:2 0:216,0:.:216:0.0:0 +20 30296664 . G C . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:203,7:29.0:210:0.033 0:112,0:.:112:0.0 +20 30309960 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:497,24:33.0:521:0.046:2 0:387,0:.:387:0.0:0 +20 31016119 rs6087903 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1069,153:30.0:1222:0.125:2 0:924,1:.:925:0.001081:0 +20 31019299 . C T . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:676,66:29.0:742:0.089 0:494,2:.:497:0.004032 +20 39704995 rs6072262 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:137,26:30.0:163:0.16:2 0:136,0:.:136:0.0:0 +20 39743905 rs6072275 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:156,22:30.0:178:0.124:2 0:79,0:.:79:0.0:0 +20 39751809 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:689,36:31.0:725:0.05:2 0:459,0:.:459:0.0:0 +20 40709305 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:40,5:29.0:45:0.111:2 0:12,0:.:12:0.0:0 +20 40714218 rs74355524 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:74,6:30.0:80:0.075:2 0:30,0:.:30:0.0:0 +20 40714305 rs143180826 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:270,58:31.0:328:0.177:2 0:159,0:.:159:0.0:0 +20 40714307 rs3092662 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:233,103:30.0:336:0.307:2 0:169,0:.:169:0.0:0 +20 40738926 rs148680893 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:311,44:30.0:355:0.124:2 0:190,0:.:190:0.0:0 +20 40746918 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:93,25:30.0:119:0.212:2 0:41,0:.:41:0.0:0 +20 40748532 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:423,21:30.0:444:0.047:2 0:270,0:.:270:0.0:0 +20 40748802 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:57,5:31.0:62:0.081:2 0:23,0:.:23:0.0:0 +20 40979469 rs187458546 A T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:81,20:30.0:101:0.198:2 0:56,0:.:56:0.0:0 +20 41101067 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:717,69:29.0:786:0.088:2 0:472,0:.:472:0.0:0 +20 46256424 rs6094752 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1101,357:30.0:1459:0.245:2 0:948,0:.:950:0.0:0 +20 46271008 rs147647230 G A . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:1533,211:30.0:1745:0.121 0:1049,4:.:1055:0.003799 +20 46275917 rs149561356 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1648,117:30.0:1765:0.066:2 0:1063,0:.:1063:0.0:0 +20 46277834 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1141,84:31.0:1226:0.069:2 0:828,0:.:829:0.0:0 +20 46279842 . G A . PASS FAILURE_REASON=nearby_gap_events,possible_contamination,alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:820,13:30.0:833:0.016 0:596,4:.:600:0.006667 +20 54945145 rs34189236 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:340,97:30.0:437:0.222:2 0:212,0:.:212:0.0:0 +20 57428287 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:766,65:31.0:831:0.078:2 0:398,0:.:399:0.0:0 +21 11021107 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:1989,130:31.0:2119:0.061:2 0:2036,0:.:2036:0.0:0 +21 11021189 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:2000,67:29.0:2067:0.032 0:1911,6:.:1919:0.00313 +21 11029526 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:235,9:32.0:244:0.037:2 0:239,0:.:239:0.0:0 +21 11047650 . C T . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:934,9:28.0:943:0.009544 0:800,0:.:801:0.0 +21 11049346 . C T . PASS FAILURE_REASON=None GT:AD:BQ:DP:FA 0/1:181,10:30.0:191:0.052 0:177,3:.:180:0.017 +21 31384240 rs17793045 C T . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:249,16:31.0:265:0.06 0:219,2:.:221:0.00905 +21 36164388 . G C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:23,9:31.0:33:0.281:2 0:21,0:.:21:0.0:0 +21 39795279 . A T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:387,31:31.0:418:0.074:2 0:288,0:.:288:0.0:0 +21 42842591 rs61735794 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:705,24:31.0:731:0.033:2 0:587,1:.:588:0.001701:0 +21 42860532 rs117696554 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:126,8:30.0:134:0.06:2 0:71,0:.:72:0.0:0 +21 42866297 rs61735793 G A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:415,12:31.0:427:0.028:2 0:327,1:.:328:0.003049:0 +21 42867003 . A T . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:246,116:30.0:362:0.32 0:318,0:.:318:0.0 +21 42872398 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:745,76:31.0:821:0.093:2 0:650,0:.:651:0.0:0 +21 42878780 . T G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:463,42:31.0:506:0.083:2 0:372,0:.:372:0.0:0 +21 43124132 rs73906207 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:41,18:32.0:59:0.305:2 0:32,0:.:32:0.0:0 +21 43124281 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:31,6:33.0:37:0.162:2 0:14,0:.:15:0.0:0 +21 44524290 rs1065145 A C . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:38,22:31.0:60:0.367 0:42,2:.:44:0.045 +21 45649498 rs61377223 C T . PASS DB;FAILURE_REASON=possible_contamination,clustered_read_position GT:AD:BQ:DP:FA 0/1:204,6:29.0:210:0.029 0:166,1:.:167:0.005988 +21 45649748 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:541,71:30.0:613:0.116:2 0:551,0:.:551:0.0:0 +21 45651275 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:713,113:29.0:826:0.137 0:700,3:.:703:0.004267 +22 17519579 rs5748829 A G . PASS DB;FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:89,40:33.0:129:0.31 0:103,3:.:106:0.028 +22 24176232 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:278,22:31.0:300:0.073:2 0:189,0:.:189:0.0:0 +22 26388019 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:57,7:31.0:64:0.109:2 0:40,0:.:40:0.0:0 +22 29120915 rs17881298 T A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:202,27:30.0:229:0.118:2 0:202,1:.:203:0.004926:0 +22 29691910 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:292,47:31.0:340:0.139:2 0:269,0:.:270:0.0:0 +22 41525892 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:368,19:33.0:387:0.049:2 0:341,0:.:342:0.0:0 +22 41542838 rs9611506 T A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:236,26:30.0:262:0.099:2 0:273,0:.:273:0.0:0 +22 41562785 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:31,10:32.0:41:0.244:2 0:47,0:.:47:0.0:0 +22 41574383 rs1046088 A C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:673,67:31.0:740:0.091:2 0:720,0:.:720:0.0:0 +X 1314857 . G A . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:140,58:30.0:198:0.293 0:245,14:.:259:0.054 +X 1314858 . G T . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:141,60:31.0:201:0.299 0:246,15:.:261:0.057 +X 1325301 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:201,11:30.0:212:0.052:2 0:302,0:.:302:0.0:0 +X 1325426 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:224,106:31.0:330:0.321:2 0:469,0:.:469:0.0:0 +X 22516183 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:35,12:27.0:47:0.255:2 0:35,0:.:35:0.0:0 +X 39930099 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:141,9:30.0:150:0.06:2 0:119,0:.:119:0.0:0 +X 39933358 . G A . PASS FAILURE_REASON=possible_contamination GT:AD:BQ:DP:FA 0/1:563,6:29.0:569:0.011 0:509,1:.:510:0.001961 +X 44896832 . C G . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:196,120:32.0:316:0.38 0:440,2:.:442:0.004525 +X 44896888 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:307,162:29.0:471:0.345:2 0:693,0:.:694:0.0:0 +X 47430627 . T G . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:144,6:31.0:150:0.04 0:161,1:.:162:0.006173 +X 53246599 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:34,13:32.0:47:0.277:2 0:41,0:.:41:0.0:0 +X 63415940 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:63,16:30.0:79:0.203:2 0:37,0:.:38:0.0:0 +X 63425821 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:127,42:30.0:170:0.249:2 0:143,0:.:145:0.0:0 +X 66766359 . C T . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:57,26:29.0:84:0.313 0:52,2:.:55:0.037 +X 66943769 . C A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:147,12:29.0:159:0.075:2 0:108,0:.:108:0.0:0 +X 70347614 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:70,15:30.0:85:0.176:2 0:63,0:.:63:0.0:0 +X 70352491 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:121,53:30.0:174:0.305:2 0:70,0:.:70:0.0:0 +X 70356829 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:597,93:32.0:690:0.135:2 0:608,0:.:609:0.0:0 +X 74803898 rs5937404 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:145,49:31.0:194:0.253:2 0:201,0:.:201:0.0:0 +X 76939830 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:484,42:33.0:526:0.08:2 0:634,0:.:634:0.0:0 +X 100057572 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:367,133:30.0:500:0.266:2 0:539,0:.:540:0.0:0 +X 100615505 . G T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:220,39:31.0:259:0.151:2 0:239,0:.:239:0.0:0 +X 122035670 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:10,3:32.0:13:0.231:2 0:13,0:.:13:0.0:0 +X 123159533 rs79769028 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:58,8:32.0:66:0.121:2 0:29,0:.:29:0.0:0 +X 123183965 rs147386628 C G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:155,17:31.0:172:0.099:2 0:116,0:.:116:0.0:0 +X 123184027 rs7063522 C T . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:386,39:31.0:425:0.092:2 0:355,0:.:356:0.0:0 +X 123184284 rs74386199 T A . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:74,10:31.0:84:0.119:2 0:49,0:.:49:0.0:0 +X 123191922 rs76876596 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:109,15:29.0:124:0.121:2 0:68,0:.:68:0.0:0 +X 123217527 rs75515623 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:75,12:32.0:87:0.138:2 0:31,0:.:31:0.0:0 +X 139479797 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:100,22:30.0:122:0.18:2 0:74,0:.:74:0.0:0 +Y 4971352 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:0,5:31.0:5:1.0:2 0:69,0:.:69:0.0:0 +MT 178 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:22,18:32.0:40:0.45:2 0:12,0:.:12:0.0:0 +MT 477 rs41442247 T C . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:27,18:32.0:45:0.4:2 0:32,0:.:32:0.0:0 +MT 533 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:37,5:33.0:42:0.119:2 0:28,0:.:28:0.0:0 +MT 4917 rs28357980 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:18,17:31.0:35:0.486:2 0:28,0:.:28:0.0:0 +MT 16019 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:20,3:32.0:23:0.13:2 0:15,0:.:15:0.0:0 +MT 16163 rs41479950 A G . PASS DB;SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:18,9:32.0:27:0.333:2 0:25,0:.:25:0.0:0 +MT 16186 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:23,9:31.0:32:0.281:2 0:23,0:.:23:0.0:0 +MT 16263 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:20,27:32.0:47:0.574:2 0:22,0:.:22:0.0:0 +MT 16316 . A G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:19,24:31.0:43:0.558:2 0:20,0:.:20:0.0:0 +GL000220.1 119409 . C T . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:45,6:21.0:51:0.118 0:84,3:.:87:0.034 +GL000220.1 119911 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:22,5:29.0:27:0.185:2 0:36,0:.:37:0.0:0 +GL000220.1 119967 . T C . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:31,4:32.0:35:0.114:2 0:48,1:.:49:0.02:0 +GL000220.1 119970 . C T . PASS FAILURE_REASON=alt_allele_in_normal GT:AD:BQ:DP:FA 0/1:29,8:29.0:37:0.216 0:44,4:.:49:0.083 +GL000220.1 120319 . C T . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:22,3:30.0:25:0.12:2 0:33,1:.:34:0.029:0 +GL000220.1 125098 . C G . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:23,4:31.0:27:0.148:2 0:47,1:.:48:0.021:0 +GL000220.1 126307 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:10,6:31.0:16:0.375:2 0:14,0:.:14:0.0:0 +GL000220.1 133613 . T A . PASS FAILURE_REASON=nearby_gap_events GT:AD:BQ:DP:FA 0/1:73,7:26.0:80:0.088 0:97,0:.:99:0.0 +GL000220.1 137741 . G A . PASS SOMATIC;VT=SNP;FAILURE_REASON=None GT:AD:BQ:DP:FA:SS 0/1:79,6:29.0:85:0.071:2 0:77,0:.:77:0.0:0 diff --git a/mutect/filter_mutect.py b/mutect/filter_mutect.py index bce04dd..d6b3767 100644 --- a/mutect/filter_mutect.py +++ b/mutect/filter_mutect.py @@ -2,7 +2,7 @@ ''' @Description : This tool helps to filter muTect v1.14 txt and vcf through command line. @Created : 07/17/2016 -@Updated : 03/17/2017 +@Updated : 04/18/2017 @author : Ronak H Shah ''' @@ -26,6 +26,7 @@ pass try: import vcf + from vcf.parser import _Info as VcfInfo, field_counts as vcf_field_counts except ImportError: logger.fatal("filter_mutect: pyvcf is not installed, please install pyvcf as it is required to run the mapping.") sys.exit(1) @@ -68,6 +69,7 @@ def RunStdFilter(args): vcf_out = vcf_out + "_STDfilter.vcf" txt_out = txt_out + "_STDfilter.txt" vcf_reader = vcf.Reader(open(args.inputVcf, 'r')) + vcf_reader.infos['FAILURE_REASON'] = VcfInfo('FAILURE_REASON', '1', 'String', 'Failure Reason from MuTect text File') vcf_writer = vcf.Writer(open(vcf_out, 'w'), vcf_reader) txtDF = pd.read_table(args.inputTxt, skiprows=1, low_memory=False) txt_fh = open(txt_out, "wb") @@ -149,6 +151,10 @@ def RunStdFilter(args): for record in vcf_reader: key_for_tracking = str(record.CHROM) + ":" + str(record.POS) + ":" + str(record.REF) + ":" + str(record.ALT[0]) if(key_for_tracking in keepDict): + failure_reason = keepDict.get(key_for_tracking) + if(failure_reason == "KEEP"): + failure_reason = "None" + record.add_info('FAILURE_REASON', failure_reason) if(record.FILTER == "PASS"): vcf_writer.write_record(record) diff --git a/pindel/filter_pindel.py b/pindel/filter_pindel.py index 10ab0c9..a5daa52 100644 --- a/pindel/filter_pindel.py +++ b/pindel/filter_pindel.py @@ -2,7 +2,7 @@ """ @Description : This tool helps to filter pindel v0.2.5a7 vcf through command line. @Created : 07/17/2014 -@Updated: 03/17/2017 +@Updated: 04/18/2017 @author : Ronak H Shah """ @@ -26,6 +26,7 @@ pass try: import vcf + from vcf.parser import _Format as VcfFormat, field_counts as vcf_field_counts except ImportError: logger.fatal("filter_pindel: pyvcf is not installed, please install pyvcf as it is required to run the mapping.") sys.exit(1) @@ -157,6 +158,7 @@ def RunStdFilter(args): vcf_out = vcf_out + "_STDfilter.vcf" txt_out = txt_out + "_STDfilter.txt" vcf_reader = vcf.Reader(open(args.inputVcf, 'r')) + vcf_reader.formats['DP'] = VcfFormat('DP', '1', 'Integer', 'Total coverage at the site') vcf_writer = vcf.Writer(open(vcf_out, 'w'), vcf_reader) txt_fh = open(txt_out, "wb") allsamples = vcf_reader.samples diff --git a/requirements.txt b/requirements.txt index 66609cb..fc785e6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ nose==1.3.7 -pyvcf==0.6.8 +pyvcf==0.6.7 pandas==0.16.2 coloredlogs==5.2 codecov==2.0.5 diff --git a/setup.py b/setup.py index e62395e..8338b95 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ setup( name='basicfiltering', - version='0.1.3', + version='0.1.4', description='Package for filtering multiple variant calling tools', long_description=readme, author='Ronak Shah',