Hi there.
I just noticed a weird issue, which may or may not be a bug. I attached a single variant in a code block below. The workflow is pretty standard, call variants on samples, merge to generate site list, then recall with forced sites. I notice that some samples are getting GT calls in the format field, even though they have a "NotGenotyped" filter associated with them (see below). It's straightforward enough for me to just set those genotypes to "./.", but I figured I'd let you know in case it is a bug.
[quser13::/projects/b1059/workflows/strelka-nf/results] π bcftools view --regions III:3529601-3550320 pruned_recalled.vcf.gz | grep 3545101
III 3545101 . CA C,CAA 3070 . CIGAR=1M1D,1M1I;IDREP=8,10;MQ=50;REFREP=9,9;RU=A,A GT:AD:ADF:ADR:DPI:FT:GQ:GQX:PL 0/0:22,0:16,0:6,0:23:PASS:61:61:. 0/0:32,0:25,0:7,0:38:PASS:91:91:. 0/0:29,0:25,0:4,0:36:PASS:84:84:. 0/0:47,0:36,0:11,0:50:PASS:99:137:. 0/0:24,0:15,0:9,0:25:PASS:68:68:. 0/0:61,0:47,0:14,0:63:PASS:99:176:. 0/0:12,0:9,0:3,0:12:PASS:33:33:. 0/0:30,0:21,0:9,0:33:PASS:85:85:. 0/0:26,0:15,0:11,0:27:PASS:75:75:. 0/0:43,0:30,0:13,0:46:PASS:99:123:. ./.:.:.:.:.:NotGenotyped:.:.:0 0/0:39,0:28,0:11,0:43:PASS:99:112:. 0/0:19,0:10,0:9,0:20:PASS:53:53:. 2/2:.:.:.:.:NotGenotyped:.:.:999 2/2:.:.:.:.:NotGenotyped:.:.:811 2/2:.:.:.:.:NotGenotyped:.:.:840 0/0:11,0:10,0:1,0:12:PASS:30:30:. 2/2:.:.:.:.:NotGenotyped:.:.:881 0/0:38,0:23,0:15,0:42:PASS:99:110:. 0/0:20,0:13,0:7,0:20:PASS:57:57:. 2/2:.:.:.:.:NotGenotyped:.:.:999 2/2:.:.:.:.:NotGenotyped:.:.:425 2/2:.:.:.:.:NotGenotyped:.:.:447 0/0:38,0:29,0:9,0:39:PASS:99:109:. 0/0:41,0:26,0:15,0:44:PASS:99:119:. 2/2:.:.:.:.:NotGenotyped:.:.:899 0/0:11,0:9,0:2,0:12:PASS:30:30:. 0/0:47,0:29,0:18,0:51:PASS:99:136:. 0/2:21,0:14,0:7,0:23:PASS:60:60:. 2/2:.:.:.:.:NotGenotyped:.:.:322 0/0:35,0:29,0:6,0:39:PASS:99:102:. 0/0:20,0:16,0:4,0:22:PASS:56:56:. 0/0:20,0:10,0:10,0:26:PASS:57:57:. 0/0:11,0:9,0:2,0:11:PASS:30:30:. 2/2:.:.:.:.:NotGenotyped:.:.:264 0/0:28,0:17,0:11,0:29:PASS:81:81:. 0/0:33,0:17,0:16,0:42:PASS:96:96:. 0/0:28,0:16,0:12,0:31:PASS:81:81:. 0/0:26,0:13,0:13,0:27:PASS:72:72:. 0/0:27,0:15,0:12,0:28:PASS:75:75:. 0/0:63,0:32,0:31,0:66:PASS:99:177:. 0/0:30,0:16,0:14,0:32:PASS:81:81:. 0/0:46,0:27,0:19,0:49:PASS:99:129:. 0/0:20,0:9,0:11,0:22:PASS:57:57:. 0/0:21,0:13,0:8,0:22:PASS:57:57:. 0/0:78,0:38,0:40,0:84:PASS:99:225:. 0/0:33,0:14,0:19,0:34:PASS:96:96:. 0/0:77,1:44,1:33,0:80:PASS:99:208:. 0/0:73,0:34,0:39,0:77:PASS:99:216:. 0/0:23,0:11,0:12,0:23:PASS:66:66:. 0/0:35,0:19,0:16,0:39:PASS:97:97:. 0/0:52,0:22,0:30,0:62:PASS:99:146:. 0/0:52,0:32,0:20,0:56:PASS:99:148:. 0/0:30,0:17,0:13,0:31:PASS:87:87:. 0/0:37,0:16,0:21,0:37:PASS:99:108:. 0/0:34,0:16,0:18,0:38:PASS:96:96:. 0/0:22,0:8,0:14,0:24:PASS:60:60:. 0/0:25,0:9,0:16,0:31:PASS:72:72:. 0/0:55,0:29,0:26,0:60:PASS:99:162:. 0/0:31,0:15,0:16,0:32:PASS:90:90:. 0/0:61,0:27,0:34,0:64:PASS:99:174:. 0/0:40,0:25,0:15,0:42:PASS:99:117:. 0/0:27,0:14,0:13,0:31:PASS:75:75:. ./.:.:.:.:.:NotGenotyped:.:.:0 0/0:75,0:35,0:40,0:80:PASS:99:212:. 0/0:64,0:32,0:32,0:76:PASS:99:182:. 0/0:29,0:17,0:12,0:32:PASS:82:82:.0/0:21,0:11,0:10,0:21:PASS:58:58:. 0/2:2,0:0,0:2,0:2:LowDepth;LowGQX:5:5:. 0/0:24,0:17,0:7,0:24:PASS:69:69:. 2/2:.:.:.:.:NotGenotyped:.:.:189 0/0:28,0:20,0:8,0:32:PASS:78:78:. 0/0:56,0:43,0:13,0:61:PASS:99:161:. 2/2:.:.:.:.:NotGenotyped:.:.:999 2/2:.:.:.:.:NotGenotyped:.:.:902 0/0:14,0:10,0:4,0:14:PASS:38:38:. 2/2:.:.:.:.:NotGenotyped:.:.:999 0/0:36,0:29,0:7,0:38:PASS:99:104:. 0/0:37,0:20,0:17,0:40:PASS:99:105:. 0/0:49,0:35,0:14,0:55:PASS:99:141:. 0/0:13,0:8,0:5,0:14:PASS:36:36:. 0/0:25,0:18,0:7,0:27:PASS:68:68:. 2/2:.:.:.:.:NotGenotyped:.:.:807 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0/1:13,1:9,1:4,0:16:LowGQX:26:0:. 2/2:.:.:.:.:NotGenotyped:.:.:999 0/0:21,0:14,0:7,0:24:PASS:58:58:. 0/0:32,0:25,0:7,0:35:PASS:92:92:. 0/0:36,0:27,0:9,0:40:PASS:99:102:. 0/0:55,0:45,0:10,0:59:PASS:99:159:. 0/0:35,0:28,0:7,0:38:PASS:99:100:. 0/0:20,0:17,0:3,0:20:PASS:55:55:. 0/0:58,0:48,0:10,0:67:PASS:99:169:. 0/0:15,0:12,0:3,0:20:PASS:41:41:. 0/0:33,0:31,0:2,0:39:PASS:93:93:. 0/0:50,0:40,0:10,0:56:PASS:99:146:. 0/0:36,0:32,0:4,0:41:PASS:99:105:. 0/0:37,0:29,0:8,0:40:PASS:99:107:. 2/2:.:.:.:.:NotGenotyped:.:.:781 0/0:39,0:37,0:2,0:43:PASS:99:112:. 0/0:31,0:21,0:10,0:35:PASS:88:88:. 0/0:37,0:33,0:4,0:39:PASS:99:107:. 0/0:29,0:24,0:5,0:34:PASS:82:82:. 0/0:18,0:14,0:4,0:24:PASS:51:51:. 0/0:37,0:18,0:19,0:41:PASS:99:107:. 0/0:40,0:26,0:14,0:44:PASS:99:113:. 0/0:36,0:29,0:7,0:42:PASS:99:103:. 2/2:.:.:.:.:NotGenotyped:.:.:339 2/2:.:.:.:.:NotGenotyped:.:.:72 0/0:6,0:4,0:2,0:6:LowGQX:14:14:. 0/2:25,0:14,0:11,0:26:PASS:72:72:. 0/0:15,0:10,0:5,0:15:PASS:40:40:. 0/0:9,0:5,0:4,0:11:PASS:24:24:. 2/2:.:.:.:.:NotGenotyped:.:.:221 2/2:.:.:.:.:NotGenotyped:.:.:317 0/0:22,0:14,0:8,0:25:PASS:61:61:. 0/2:10,0:6,0:4,0:10:PASS:26:26:. 0/0:21,0:8,0:13,0:24:PASS:59:59:. 2/2:.:.:.:.:NotGenotyped:.:.:194 2/2:.:.:.:.:NotGenotyped:.:.:999 0/2:1,0:1,0:0,0:2:LowDepth;LowGQX:3:2:. 0/0:7,0:4,0:3,0:7:PASS:18:18:. 0/0:7,0:4,0:3,0:7:PASS:18:18:. ./2:.:.:.:.:NotGenotyped:.:.:875 0/0:47,0:33,0:14,0:49:PASS:99:135:. 0/0:14,0:7,0:7,0:16:PASS:39:39:. 0/0:27,0:14,0:13,0:31:PASS:74:74:. 0/0:20,0:10,0:10,0:23:PASS:55:55:. 0/0:49,0:40,0:9,0:55:PASS:99:141:. 0/0:40,0:35,0:5,0:44:PASS:99:115:. 0/0:35,0:28,0:7,0:35:PASS:99:100:. 0/0:16,0:10,0:6,0:16:PASS:45:45:. 0/0:15,0:8,0:7,0:16:PASS:41:41:. 2/2:.:.:.:.:NotGenotyped:.:.:999 0/0:25,0:19,0:6,0:25:PASS:69:69:. 0/0:43,0:35,0:8,0:44:PASS:99:123:. 0/0:26,0:20,0:6,0:27:PASS:73:73:. 2/2:.:.:.:.:NotGenotyped:.:.:495 0/0:16,0:8,0:8,0:20:PASS:45:45:. 2/2:.:.:.:.:NotGenotyped:.:.:680 2/2:.:.:.:.:NotGenotyped:.:.:460 ./2:.:.:.:.:NotGenotyped:.:.:999 0/1:61,2:45,2:16,0:70:LowGQX:49:2:. 2/2:.:.:.:.:NotGenotyped:.:.:999 0/0:11,0:9,0:2,0:12:PASS:30:30:. 0/0:8,0:5,0:3,0:10:PASS:20:20:. 0/0:23,0:15,0:8,0:25:PASS:66:66:. 2/2:.:.:.:.:NotGenotyped:.:.:999 0/0:43,0:29,0:14,0:48:PASS:99:123:. 0/0:41,0:26,0:15,0:47:PASS:99:118:. 2/2:.:.:.:.:NotGenotyped:.:.:627 0/0:22,0:17,0:5,0:24:PASS:63:63:. 0/0:40,0:32,0:8,0:41:PASS:99:114:. 0/0:42,0:32,0:10,0:46:PASS:99:122:. 0/0:16,0:11,0:5,0:17:PASS:45:45:. 0/0:42,0:30,0:12,0:45:PASS:99:120:. 2/2:.:.:.:.:NotGenotyped:.:.:999 0/0:7,0:3,0:4,0:9:PASS:18:18:. 0/0:38,0:28,0:10,0:45:PASS:99:109:. 0/0:50,0:31,0:19,0:59:PASS:99:143:. 0/0:42,0:28,0:14,0:47:PASS:99:122:. 0/0:53,0:38,0:15,0:56:PASS:99:155:. 0/0:44,0:32,0:12,0:49:PASS:99:126:. 0/0:34,0:22,0:12,0:38:PASS:95:95:. 0/0:11,0:7,0:4,0:12:PASS:30:30:. 0/0:24,0:18,0:6,0:27:PASS:67:67:. 0/0:28,0:20,0:8,0:32:PASS:80:80:. 0/0:57,0:37,0:20,0:65:PASS:99:164:. 0/0:33,0:25,0:8,0:40:PASS:94:94:. 0/0:32,0:23,0:9,0:32:PASS:91:91:. 0/0:30,0:18,0:12,0:31:PASS:85:85:. 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