Dear Team,
I am running joint calling (according to Best Practices). I have ~800 samples from 3 different centres.First I run CombineGVCFs on cases from batch1(~130samples), controls from batch1(~130samples), cases from batch2 (~130samples) etc. Next, I run GenotypeGVCFs on these 6 files.
According to my final file I have 19 HOM and 32 HET in chr1:47571951.
However, when I looked at the individual g.vcfs ( generated by HaplotypeCaller, --emitConfidence GVCF) the specific variant is recorded in 1/800 g.vcfs (from batch1).
1 47571951 . T TTA, 0 . DP=25;MLEAC=0,0;MLEAF=0.00,0.00;MQ=58.61;MQ0=0 GT:AD:DP:GQ:PL:SB 0/0:21,0,0:21:63:0,63,735,63,735,735:8,13,0,0
but when I looked that the bam file, there is nothing.
After running CombineGVCFs with other files from batch1 controls I have this:
1 47571951 . T TTA, . . DP=8537;MQ=58.61;MQ0=0 GT:AD:DP:MIN_DP:PL:SB./.:.:80:63:0,86,1514,86,1514,1514 ./.:.:60:46:0,110,1343,110,1343,1343 ./.:.:59:50:0,95,1202,95,1202,1202 ./.:.:91:65:0,115,1541,115,1541,1541./.:.:90:74:0,120,1800,120,1800,1800 ./.:.:49:38:0,70,921,70,921,921 ./.:.:52:40:0,88,1080,88,1080,1080 ./.:.:54:46:0,61,1216,61,1216,1216 ./.:.:63:45:0,106,1119,106,1119,1119 ./.:.:46:36:0,78,873,78,873,873 ./.:.:48:35:0,67,771,67,771,771 ./.:.:77:70:0,85,1741,85,1741,1741 ./.:.:64:43:0,81,948,81,948,948 ./.:.:65:51:0,120,1800,120,1800,1800 ./.:.:90:70:0,110,1701,110,1701,1701 ./.:.:66:44:0,114,1003,114,1003,1003 ./.:.:63:57:0,116,1376,116,1376,1376 ./.:.:57:52:0,113,1547,113,1547,1547 ./.:.:74:51:0,93,1122,93,1122,1122 ./.:.:81:53:0,73,1273,73,1273,1273 ./.:.:33:25:0,69,710,69,710,710 ./.:.:70:63:0,120,1800,120,1800,1800 ./.:.:45:34:0,69,830,69,830,830 ./.:.:64:47:0,75,1155,75,1155,1155 ./.:.:59:28:0,72,780,72,780,780 ./.:.:61:45:0,93,1516,93,1516,1516 ./.:.:52:45:0,66,1240,66,1240,1240 ./.:.:77:62:0,120,1800,120,1800,1800 ./.:.:55:48:0,86,1358,86,1358,1358 ./.:.:86:61:0,64,1553,64,1553,1553 ./.:.:106:86:0,120,1800,120,1800,1800 ./.:.:86:84:0,120,1800,120,1800,1800 ./.:.:65:51:0,65,1133,65,1133,1133 ./.:.:71:53:0,104,1392,104,1392,1392 ./.:.:56:46:0,110,1197,110,1197,1197 ./.:.:70:51:0,88,1222,88,1222,1222 ./.:.:50:40:0,84,1260,84,1260,1260 ./.:.:58:41:0,95,1017,95,1017,1017 ./.:.:73:62:0,120,1800,120,1800,1800 ./.:.:48:41:0,87,1049,87,1049,1049 ./.:.:14:12:0,21,361,21,361,361 ./.:.:83:55:0,120,1800,120,1800,1800 ./.:.:58:50:0,90,1350,90,1350,1350 ./.:.:63:36:0,107,875,107,875,875 ./.:.:69:68:0,120,1800,120,1800,1800 ./.:.:69:55:0,120,1800,120,1800,1800 ./.:.:51:42:0,75,1348,75,1348,1348 ./.:.:77:41:0,79,1120,79,1120,1120 ./.:.:57:45:0,109,1051,109,1051,1051 ./.:.:50:36:0,69,984,69,984,984 ./.:.:68:58:0,120,1800,120,1800,1800 ./.:.:42:31:0,62,741,62,741,741 ./.:.:49:35:0,80,878,80,878,878 ./.:.:62:50:0,117,1755,117,1755,1755 ./.:.:60:55:0,89,1485,89,1485,1485 ./.:.:53:39:0,68,990,68,990,990 ./.:.:62:55:0,120,1800,120,1800,1800 ./.:.:58:51:0,64,1167,64,1167,1167 ./.:.:40:23:0,66,990,66,990,990 ./.:.:75:63:0,94,1800,94,1800,1800 ./.:.:73:60:0,119,1800,119,1800,1800 ./.:.:65:41:0,72,983,72,983,983 ./.:.:74:66:0,84,1669,84,1669,1669 ./.:.:82:67:0,120,1800,120,1800,1800 ./.:.:50:39:0,110,1071,110,1071,1071 ./.:.:64:48:0,116,1495,116,1495,1495 ./.:.:65:40:0,104,1095,104,1095,1095 ./.:.:33:32:0,71,851,71,851,851 ./.:.:62:50:0,75,1383,75,1383,1383 ./.:.:71:54:0,119,1505,119,1505,1505./.:.:43:28:0,62,681,62,681,681 ./.:.:71:66:0,93,1645,93,1645,1645 ./.:.:38:33:0,61,859,61,859,859 ./.:.:76:47:0,101,1121,101,1121,1121 ./.:.:65:47:0,71,1078,71,1078,1078 ./.:.:58:42:0,65,1144,65,1144,1144 ./.:.:70:59:0,111,1785,111,1785,1785 ./.:.:33:32:0,72,1080,72,1080,1080 ./.:.:43:37:0,84,1260,84,1260,1260 ./.:.:99:55:0,109,1361,109,1361,1361 ./.:.:53:42:0,106,990,106,990,990 ./.:.:55:32:0,80,769,80,769,769 ./.:.:75:41:0,90,1065,90,1065,1065 ./.:.:60:50:0,114,1710,114,1710,1710 ./.:.:98:78:0,120,1800,120,1800,1800 ./.:.:80:48:0,94,1089,94,1089,1089 ./.:.:73:43:0,80,1061,80,1061,1061 ./.:.:38:31:0,66,697,66,697,697 ./.:.:52:33:0,98,890,98,890,890 ./.:.:45:43:0,101,1257,101,1257,1257 ./.:.:43:34:0,65,680,65,680,680 ./.:.:86:82:0,120,1800,120,1800,1800 ./.:.:44:38:0,62,960,62,960,960 ./.:.:61:54:0,89,1393,89,1393,1393 ./.:.:43:37:0,81,989,81,989,989 ./.:.:87:67:0,120,1800,120,1800,1800 ./.:.:54:35:0,80,892,80,892,892 ./.:.:65:53:0,93,1181,93,1181,1181 ./.:.:66:58:0,120,1800,120,1800,1800 ./.:.:57:44:0,91,971,91,971,971 ./.:.:53:45:0,80,1246,80,1246,1246 ./.:.:62:49:0,95,1159,95,1159,1159 ./.:.:53:40:0,95,969,95,969,969 ./.:.:86:72:0,120,1800,120,1800,1800./.:21,0,0:21:.:0,63,735,63,735,735:8,13,0,0 ./.:.:54:45:0,120,1800,120,1800,1800 ./.:.:74:63:0,120,1800,120,1800,1800 ./.:.:74:52:0,117,1755,117,1755,1755 ./.:.:61:44:0,79,1273,79,1273,1273 ./.:.:61:54:0,104,1617,104,1617,1617 ./.:.:89:59:0,100,1721,100,1721,1721 ./.:.:92:65:0,67,1504,67,1504,1504 ./.:.:67:52:0,93,1450,93,1450,1450 ./.:.:86:73:0,120,1800,120,1800,1800 ./.:.:62:51:0,81,1437,81,1437,1437 ./.:.:59:47:0,72,1161,72,1161,1161 ./.:.:67:50:0,74,1800,74,1800,1800 ./.:.:35:32:0,71,849,71,849,849 ./.:.:77:71:0,108,1664,108,1664,1664 ./.:.:35:28:0,63,809,63,809,809 ./.:.:62:45:0,88,1208,88,1208,1208 ./.:.:76:57:0,70,1187,70,1187,1187 ./.:.:51:35:0,63,783,63,783,783 ./.:.:63:53:0,120,1800,120,1800,1800 ./.:.:39:36:0,86,954,86,954,954 ./.:.:56:40:0,68,1010,68,1010,1010 ./.:.:62:42:0,84,1159,84,1159,1159 ./.:.:69:43:0,99,1264,99,1264,1264 ./.:.:69:37:0,66,870,66,870,870 ./.:.:138:90:0,88,1800,88,1800,1800 ./.:.:52:47:0,66,1334,66,1334,1334 ./.:.:66:51:0,95,1155,95,1155,1155 ./.:.:61:35:0,103,953,103,953,953 ./.:.:74:73:0,120,1800,120,1800,1800 ./.:.:40:36:0,62,954,62,954,954 ./.:.:95:79:0,89,1800,89,1800,1800 ./.:.:74:53:0,63,1149,63,1149,1149 ./.:.:66:63:0,112,1560,112,1560,1560 ./.:.:70:67:0,120,1800,120,1800,1800 ./.:.:123:106:0,120,1800,120,1800,1800 ./.:.:32:32:0,81,1215,81,1215,1215 ./.:.:66:40:0,97,1051,97,1051,1051 ./.:.:57:36:0,76,980,76,980,980 ./.:.:69:49:0,120,1800,120,1800,1800 ./.:.:58:43:0,93,1014,93,1014,1014 ./.:.:51:30:0,69,734,69,734,734 ./.:.:80:65:0,120,1800,120,1800,1800 ./.:.:83:71:0,120,1800,120,1800,1800 ./.:.:54:44:0,73,1209,73,1209,1209 ./.:.:46:38:0,80,961,80,961,961 ./.:.:63:56:0,97,1383,97,1383,1383 ./.:.:57:41:0,88,1337,88,1337,1337 ./.:.:70:44:0,71,1112,71,1112,1112 ./.:.:67:65:0,120,1800,120,1800,1800 ./.:.:84:74:0,120,1800,120,1800,1800 ./.:.:74:56:0,120,1800,120,1800,1800 ./.:.:46:34:0,90,918,90,918,918 ./.:.:44:34:0,67,906,67,906,906 ./.:.:29:24:0,60,793,60,793,793 ./.:.:43:27:0,76,711,76,711,711 ./.:.:91:68:0,113,1525,113,1525,1525 ./.:.:65:63:0,118,1641,118,1641,1641 ./.:.:59:41:0,102,978,102,978,978 ./.:.:101:82:0,97,1800,97,1800,1800 ./.:.:59:44:0,67,1081,67,1081,1081 ./.:.:48:37:0,62,842,62,842,842 ./.:.:50:38:0,98,959,98,959,959 ./.:.:87:72:0,120,1800,120,1800,1800 ./.:.:64:58:0,75,1535,75,1535,1535 ./.:.:33:31:0,67,910,67,910,910 ./.:.:65:39:0,61,865,61,865,865 ./.:.:84:62:0,73,1540,73,1540,1540 ./.:.:75:66:0,120,1800,120,1800,1800
And results from controls from batch3(CombineGVCFS) I have this (different variant but the same position)
1 47571951 . T . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:69:0,120,1800 ./.:62:99:52:0,73,1184 ./.:56:99:47:0,94,1143 ./.:55:99:54:0,120,1800 ./.:71:99:58:0,120,1800 ./.:41:99:39:0,61,923 ./.:37:99:36:0,80,921 ./.:30:84:30:0,65,754 ./.:28:72:25:0,69,1035 ./.:48:99:42:0,74,1047 ./.:47:99:40:0,85,950 ./.:140:99:115:0,120,1800 ./.:103:99:87:0,120,1800 ./.:173:99:126:0,120,1800 ./.:148:99:122:0,81,1800 ./.:185:99:148:0,120,1800 ./.:163:99:112:0,120,1800 ./.:174:99:136:0,120,1800 ./.:161:99:143:0,120,1800 ./.:214:99:161:0,104,1800 ./.:146:99:118:0,120,1800 ./.:181:99:136:0,120,1800 ./.:101:99:86:0,120,1800 ./.:55:99:43:0,93,1121 ./.:108:99:87:0,120,1800 ./.:174:99:121:0,85,1800 ./.:149:99:113:0,120,1800 ./.:127:99:96:0,98,1800 ./.:194:99:134:0,120,1800 ./.:149:99:128:0,120,1800 ./.:153:99:141:0,120,1800 ./.:137:99:136:0,120,1800 ./.:186:99:172:0,120,1800 ./.:42:99:33:0,61,928 ./.:69:99:48:0,112,1791 ./.:39:99:35:0,64,842 ./.:26:60:25:0,60,900 ./.:60:99:51:0,71,1230 ./.:61:99:51:0,104,1199 ./.:67:99:63:0,91,1631 ./.:63:99:57:0,120,1800 ./.:66:99:58:0,75,1619 ./.:58:99:47:0,90,1111 ./.:119:99:88:0,120,1800 ./.:103:99:80:0,120,1800 ./.:108:99:77:0,120,1800 ./.:180:99:137:0,120,1800 ./.:128:99:99:0,72,1800 ./.:61:99:56:0,62,1333 ./.:59:99:52:0,120,1800 ./.:117:99:103:0,120,1800 ./.:64:99:55:0,106,1318 ./.:62:99:41:0,66,978./.:51:99:39:0,115,967 ./.:153:99:126:0,85,1800 ./.:199:99:153:0,120,1800 ./.:144:99:121:0,120,1800 ./.:137:99:111:0,120,1800 ./.:64:99:47:0,72,1375 ./.:65:99:49:0,73,1214 ./.:45:99:44:0,110,1455 ./.:143:99:101:0,96,1800 ./.:168:99:157:0,120,1800 ./.:122:99:104:0,120,1800 ./.:156:99:123:0,120,1800 ./.:243:99:179:0,90,1800 ./.:117:99:111:0,120,1800 ./.:184:99:161:0,120,1800 ./.:149:99:145:0,120,1800 ./.:168:99:137:0,82,1800 ./.:164:99:126:0,120,1800 ./.:176:99:149:0,120,1800 ./.:129:99:97:0,120,1800 ./.:182:99:161:0,120,1800 ./.:52:99:49:0,120,1800 ./.:215:99:171:0,120,1800 ./.:217:99:182:0,120,1800 ./.:128:99:94:0,120,1800 ./.:132:99:125:0,116,1800 ./.:131:99:106:0,120,1800 ./.:152:99:133:0,120,1800 ./.:138:99:118:0,120,1800 ./.:139:99:112:0,120,1800 ./.:207:99:190:0,120,1800 ./.:163:99:133:0,120,1800 ./.:192:99:157:0,120,1800 ./.:152:99:121:0,108,1800 ./.:160:99:134:0,120,1800 ./.:204:99:168:0,120,1800 ./.:229:99:178:0,120,1800 ./.:190:99:147:0,120,1800 ./.:193:99:180:0,87,1800 ./.:256:99:246:0,120,1800 ./.:226:99:155:0,120,1800 ./.:206:99:146:0,120,1800 ./.:213:99:155:0,120,1800 ./.:214:99:154:0,120,1800 ./.:126:99:114:0,115,1800 ./.:140:99:133:0,120,1800 ./.:106:99:105:0,120,1800 ./.:156:99:124:0,91,1800 ./.:103:99:100:0,120,1800 ./. ./.:100:99:91:0,71,1800 ./.:141:99:135:0,120,1800 ./.:120:99:116:0,120,1800 ./.:102:99:87:0,79,1800 ./.:87:99:80:0,64,1800 ./.:145:99:111:0,94,1800 ./.:107:99:101:0,120,1800 ./.:104:99:84:0,120,1800 ./.:109:99:93:0,120,1800 ./.:117:99:111:0,120,1800 ./.:103:99:83:0,120,1800 ./.:92:99:62:0,80,1532 ./.:161:99:126:0,120,1800 ./.:160:99:114:0,120,1800 ./.:221:99:156:0,105,1800 ./.:104:99:83:0,120,1800 ./.:126:99:124:0,120,1800 ./.:116:99:99:0,120,1800 ./.:103:99:83:0,120,1800 ./.:136:99:108:0,120,1800 ./.:117:99:108:0,120,1800 ./.:134:99:115:0,120,1800 ./.:146:99:139:0,120,1800 ./.:137:99:103:0,120,1800 ./.:127:99:90:0,90,1800 ./.:112:99:96:0,120,1800 ./.:241:99:182:0,120,1800 ./.:144:99:126:0,120,1800 ./.:136:99:123:0,120,1800 ./.:201:99:176:0,120,1800 ./.:121:99:102:0,120,1800 ./.:31:90:26:0,62,669 ./.:87:99:61:0,120,1800 ./.:30:77:24:0,69,693 ./.:80:99:74:0,120,1800 ./.:72:99:46:0,61,996 ./.:170:99:160:0,120,1800 ./.:74:99:69:0,73,1594 ./.:93:99:71:0,115,1733 ./.:104:99:92:0,120,1800 ./.:133:99:108:0,71,1800 ./.:120:99:100:0,72,1800 ./.:145:99:134:0,120,1800 ./.:164:99:149:0,120,1800 ./.:80:99:69:0,111,1465 ./.:96:99:66:0,120,1800 ./.:146:99:129:0,120,1800 ./.:83:99:52:0,102,1127 ./.:170:99:143:0,120,1800 ./.:133:99:103:0,120,1800 ./.:129:99:112:0,120,1800 ./.:88:99:81:0,120,1800 ./.:109:99:86:0,120,1800 ./.:161:99:149:0,120,1800 ./.:211:99:162:0,95,1800 ./.:114:99:91:0,120,1800 ./.:137:99:108:0,120,1800 ./.:121:99:93:0,106,1800 ./.:118:99:99:0,120,1800 ./.:177:99:133:0,120,1800
The variant is not present in cases batch 1,2,3 and controls batch2 (in CombineGVCFs file)
When I run GenotypeGVCFs with 6 files (3 case 3 control files) I have this: According to this, the variant is present in 19 HOM and 32 HET all from batch 3.
1 47571951 . T TTA 39185.39 . AC=70;AF=0.045;AN=1554;DP=59833;FS=6.566;GQ_MEAN=107.66;GQ_STDDEV=49.77;InbreedingCoeff=0.4981;MLEAC=68;MLEAF=0.044;MQ=58.61;MQ0=0;NCC=2;QD=32.97 GT:AD:DP:GQ:PL 1/1:0,0:56:99:917,162,0 0/1:9,0:31:99:241,0,135 0/1:9,0:31:70:70,0,157 0/0:0,0:17:0:0,0,0 0/0:13,0:29:39:0,39,265 0/1:4,0:23:54:54,0,62 0/0:69,0:69:99:0,120,1800 0/0:52,0:52:73:0,73,1184 0/0:47,0:47:94:0,94,1143 0/0:54,0:54:99:0,120,1800 0/0:58,0:58:99:0,120,1800 0/1:2,0:14:19:60,0,19 0/0:3,0:8:9:0,9,53 1/1:0,0:16:47:283,47,0 0/1:3,0:14:26:57,0,260/0:39,0:39:61:0,61,923 0/0:36,0:36:80:0,80,921 0/0:30,0:30:65:0,65,754 0/0:25,0:25:69:0,69,1035 0/0:42,0:42:74:0,74,1047 0/0:40,0:40:85:0,85,950 0/1:12,0:96:50:998,0,50 0/0:35,0:81:72:0,72,842 0/1:24,0:81:99:717,0,371 0/1:32,0:110:99:726,0,512 0/1:26,0:97:99:308,0,420 0/1:15,0:69:99:652,0,179 0/0:115,0:115:99:0,120,1800 0/0:87,0:87:99:0,120,1800 0/0:126,0:126:99:0,120,1800 0/0:122,0:122:81:0,81,1800 0/0:148,0:148:99:0,120,1800 0/0:112,0:112:99:0,120,1800 0/0:46,0:98:99:0,101,1070 0/1:37,0:147:99:1242,0,569 0/0:47,0:97:56:0,56,1011 0/1:16,0:87:99:934,0,150 0/0:34,0:88:79:0,79,762 0/1:19,0:93:99:786,0,242 0/0:136,0:136:99:0,120,1800 0/0:143,0:143:99:0,120,1800 0/0:161,0:161:99:0,104,1800 0/0:118,0:118:99:0,120,1800 0/0:136,0:136:99:0,120,1800 0/1:13,0:73:99:745,0,130 0/0:25,0:49:20:0,20,574 1/1:0,0:100:99:1925,295,0 0/1:22,0:97:99:772,0,292 1/1:0,0:101:99:1906,291,0 1/1:0,0:85:99:1632,250,0 0/0:86,0:86:99:0,120,1800 0/0:43,0:43:93:0,93,1121 0/0:87,0:87:99:0,120,1800 0/0:121,0:121:85:0,85,1800 0/0:113,0:113:99:0,120,1800 0/1:10,0:63:85:664,0,85 0/0:8,0:21:19:0,19,202 0/0:17,0:39:48:0,48,323 0/0:14,0:34:14:0,14,304 0/0:28,0:57:63:0,63,711 0/0:20,0:37:59:0,59,504 0/0:96,0:96:98:0,98,1800 0/0:134,0:134:99:0,120,1800 0/0:128,0:128:99:0,120,1800 0/0:141,0:141:99:0,120,1800 0/0:136,0:136:99:0,120,1800 0/0:172,0:172:99:0,120,1800 0/0:6,0:19:5:0,5,126 0/1:3,0:12:28:28,0,52 0/0:9,0:17:3:0,3,174 ./.:4,0:4 0/0:1,0:24:3:0,3,40 1/1:0,0:60:99:1101,177,0 0/0:33,0:33:61:0,61,928 0/0:48,0:48:99:0,112,1791 0/0:35,0:35:64:0,64,842 0/0:25,0:25:60:0,60,900 0/0:14,0:20:19:0,19,293 0/0:7,0:19:21:0,21,157 0/0:8,0:14:23:0,23,187 0/0:10,0:21:30:0,30,412 0/1:5,0:27:47:265,0,47 0/0:51,0:51:71:0,71,1230 0/0:51,0:51:99:0,104,1199 0/0:63,0:63:91:0,91,1631 0/0:57,0:57:99:0,120,1800 0/0:58,0:58:75:0,75,1619 0/0:47,0:47:90:0,90,1111 0/0:45,0:79:99:0,105,1054 0/0:20,0:76:58:0,58,485 0/0:23,0:59:69:0,69,540 0/0:33,0:69:69:0,69,777 0/1:20,0:75:99:746,0,269 0/0:88,0:88:99:0,120,1800 0/0:80,0:80:99:0,120,1800 0/0:77,0:77:99:0,120,1800 0/0:137,0:137:99:0,120,1800 0/0:99,0:99:72:0,72,1800 0/1:3,0:28:20:225,0,20 0/1:8,0:33:98:292,0,98 0/0:12,0:22:35:0,35,264 0/0:7,0:12:21:0,21,167 1/1:0,0:26:51:319,51,0 0/1:3,0:26:31:245,0,31 0/0:56,0:56:62:0,62,1333 0/0:52,0:52:99:0,120,1800 0/0:103,0:103:99:0,120,1800 0/0:55,0:55:99:0,106,1318 0/0:41,0:41:66:0,66,978 0/0:39,0:39:99:0,115,967 0/1:14,0:74:99:587,0,161 0/0:16,0:50:14:0,14,340 1/1:0,0:73:99:1434,216,0 1/1:0,0:82:99:1515,239,0 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0/0:99,0:99:99:0,120,1800 0/0:90,0:90:99:0,120,1800 0/0:53,0:53:99:0,120,1800 0/0:40,0:40:81:0,81,1215 0/0:119,0:119:99:0,120,1800 0/0:100,0:100:99:0,120,1800 0/0:92,0:92:99:0,120,1800 0/0:105,0:105:99:0,120,1800 0/0:129,0:129:99:0,120,1800 0/0:99,0:99:94:0,94,1800 0/0:140,0:140:99:0,120,1800 0/0:128,0:128:99:0,120,1800 0/0:96,0:96:99:0,120,1800 0/0:99,0:99:99:0,120,1800 0/0:86,0:86:99:0,120,1800 0/0:100,0:100:99:0,120,1800 0/0:110,0:110:99:0,120,1800 0/0:125,0:125:99:0,120,1800 0/0:149,0:149:99:0,120,1800 0/0:107,0:107:99:0,120,1800 0/0:81,0:81:99:0,120,1800 0/0:105,0:105:99:0,120,1800 0/0:89,0:89:99:0,120,1800 0/0:125,0:125:99:0,120,1800 0/0:120,0:120:99:0,120,1800 0/0:52,0:52:99:0,120,1800 0/0:91,0:91:99:0,120,1800 0/0:114,0:114:99:0,120,1800 0/0:94,0:94:99:0,120,1800 0/0:74,0:74:99:0,120,1800 0/0:80,0:80:99:0,120,1800 0/0:105,0:105:99:0,120,1800 0/0:83,0:83:99:0,111,1800 0/0:86,0:86:99:0,120,1800
I am not sure, why suddenly the variant that is not recorded in the majority of individual g.vcfs and bam files appeared in the final file.
Thank you very much for your help.
an_kate