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/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/
H A DtestBasepairResolutionInput.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
115 20 10000000 . T <NON_REF> . . . GT:AD:DP:GQ:PL ./.:52,0:52:99:0,120,1800
116 20 10000001 . T <NON_REF> . . . GT:AD:DP:GQ:PL ./.:54,0:54:99:0,120,1800
117 20 10000002 . G <NON_REF> . . . GT:AD:DP:GQ:PL ./.:50,0:50:99:0,120,1800
118 20 10000003 . T <NON_REF> . . . GT:AD:DP:GQ:PL ./.:53,0:53:99:0,120,1800
119 20 10000004 . T <NON_REF> . . . GT:AD:DP:GQ:PL ./.:50,0:50:99:0,120,1800
120 20 10000005 . T <NON_REF> . . . GT:AD:DP:GQ:PL ./.:52,0:52:99:0,120,1800
156 20 10000041 . G <NON_REF> . . . GT:AD:DP:GQ:PL ./.:43,1:44:93:0,93,1465
157 20 10000042 . T <NON_REF> . . . GT:AD:DP:GQ:PL ./.:43,1:44:97:0,98,1488
158 20 10000043 . T <NON_REF> . . . GT:AD:DP:GQ:PL ./.:41,1:42:88:0,89,1446
[all …]
H A Dgvcf.basepairResolution.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
108 20 10000000 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:52,0:52:99:0,120,1800
109 20 10000001 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:54,0:54:99:0,120,1800
110 20 10000002 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:50,0:50:99:0,120,1800
111 20 10000003 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:53,0:53:99:0,120,1800
112 20 10000004 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:50,0:50:99:0,120,1800
113 20 10000005 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:52,0:52:99:0,120,1800
149 20 10000041 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:43,1:44:93:0,93,1465
150 20 10000042 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:43,1:44:97:0,98,1488
151 20 10000043 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:41,1:42:88:0,89,1446
[all …]
H A DtetraploidRun.GATK3.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
188 20 4966623 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:4:4:4:0,5,12,24,144 ./././.:5:3:3:0,4,9,1…
189 20 4966624 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:4:4:4:0,5,12,24,144 ./././.:5:3:3:0,4,9,1…
191 20 4966627 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:4:4:4:0,5,12,24,144 ./././.:4:4:4:0,5,12,…
193 20 4966630 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:4:3:4:0,4,9,18,135 ./././.:5:6:5:0,6,15,3…
197 20 4966637 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:3:2:2:0,2,6,12,77 ./././.:7:8:7:0,9,21,42…
198 20 4966638 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:3:2:2:0,2,6,12,77 ./././.:7:8:7:0,9,21,42…
199 20 4966639 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:3:2:2:0,2,6,12,77 ./././.:8:9:8:0,10,24,4…
203 20 4966654 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:2:1:1:0,1,3,6,32 ./././.:8:8:8:0,9,21,42,…
210 20 4966665 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:12:13:11:0,14,33,…
[all …]
H A DYRIoffspring.chr20snippet.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
399 20 10001432 . A <NON_REF> . . END=10001435 GT:DP:GQ:MIN_DP:PL 0/0:42:6:41:0,6,90
401 20 10001437 . A <NON_REF> . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:42:0:42:0,0,0
404 20 10001443 . C <NON_REF> . . END=10001446 GT:DP:GQ:MIN_DP:PL 0/0:40:0:37:0,0,885
596 20 10002459 . T <NON_REF> . . END=10002459 GT:DP:GQ:MIN_DP:PL 0/0:38:0:38:0,0,73
1168 20 10006824 . A <NON_REF> . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:43:0:43:0,0,0
1331 20 10008030 . A <NON_REF> . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:47:0:47:0,0,0
1359 20 10008143 . C <NON_REF> . . END=10008145 GT:DP:GQ:MIN_DP:PL 0/0:53:0:51:0,0,0
1361 20 10008148 . A <NON_REF> . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0
1404 20 10008759 . A <NON_REF> . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:42:0:42:0,0,0
[all …]
H A DnewMQcalc.combined.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
416 20 10001433 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:56:0:56:0,0,1779 ./.:42:6:41:0,6,90
418 20 10001435 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:55:0:55:0,0,1790 ./.:42:6:41:0,6,90
11202 20 10098311 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:2:6:2:0,6,80 ./.:39:0:33:0,0,0
11209 20 10098344 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:4:0:4:0,0,1 ./.:32:0:32:0,0,0
11217 20 10098357 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:3:3:3:0,3,45 ./.:23:6:23:0,6,90
11239 20 10098613 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./.:12:0:12:0,0,74
11243 20 10098617 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./.:14:0:14:0,0,6
11252 20 10098638 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:1:0:1:0,0,0 ./.:14:9:14:0,9,359
11257 20 10098647 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:1:0:1:0,0,0 ./.:16:0:16:0,0,228
[all …]
H A Dtetraploid-gvcf-1.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
184 20 4966535 . A <NON_REF> . . END=4966540 GT:DP:GQ:MIN_DP:PL 0/0/0/0:9:7:8:0,7,18,36,270
188 20 4966555 . A <NON_REF> . . END=4966563 GT:DP:GQ:MIN_DP:PL 0/0/0/0:5:3:4:0,4,9,18,135
194 20 4966607 . A <NON_REF> . . END=4966617 GT:DP:GQ:MIN_DP:PL 0/0/0/0:4:3:4:0,4,9,18,135
196 20 4966630 . C <NON_REF> . . END=4966634 GT:DP:GQ:MIN_DP:PL 0/0/0/0:4:3:4:0,4,9,18,135
197 20 4966635 . G <NON_REF> . . END=4966649 GT:DP:GQ:MIN_DP:PL 0/0/0/0:3:2:2:0,2,6,12,77
198 20 4966650 . A <NON_REF> . . END=4966664 GT:DP:GQ:MIN_DP:PL 0/0/0/0:2:1:1:0,1,3,6,32
199 20 4966665 . G <NON_REF> . . END=4966703 GT:DP:GQ:MIN_DP:PL 0/0/0/0:0:0:0:0,0,0,0,0
200 20 4966704 . G <NON_REF> . . END=4966707 GT:DP:GQ:MIN_DP:PL 0/0/0/0:1:1:1:0,1,3,6,33
201 20 4966708 . T <NON_REF> . . END=4966711 GT:DP:GQ:MIN_DP:PL 0/0/0/0:2:2:2:0,2,6,12,69
[all …]
H A Dtetraploid-gvcf-2.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
190 20 4966600 . T <NON_REF> . . END=4966601 GT:DP:GQ:MIN_DP:PL 0/0/0/0:8:7:8:0,7,18,36,270
191 20 4966602 . C <NON_REF> . . END=4966608 GT:DP:GQ:MIN_DP:PL 0/0/0/0:6:6:6:0,6,15,30,225
192 20 4966609 . A <NON_REF> . . END=4966611 GT:DP:GQ:MIN_DP:PL 0/0/0/0:6:4:6:0,5,12,24,180
193 20 4966612 . A <NON_REF> . . END=4966624 GT:DP:GQ:MIN_DP:PL 0/0/0/0:5:3:3:0,4,9,18,113
194 20 4966625 . G <NON_REF> . . END=4966627 GT:DP:GQ:MIN_DP:PL 0/0/0/0:4:4:4:0,5,12,24,159
195 20 4966628 . A <NON_REF> . . END=4966632 GT:DP:GQ:MIN_DP:PL 0/0/0/0:5:6:5:0,6,15,30,175
196 20 4966633 . T <NON_REF> . . END=4966636 GT:DP:GQ:MIN_DP:PL 0/0/0/0:6:7:6:0,7,18,36,214
197 20 4966637 . C <NON_REF> . . END=4966638 GT:DP:GQ:MIN_DP:PL 0/0/0/0:7:8:7:0,9,21,42,270
199 20 4966640 . A <NON_REF> . . END=4966645 GT:DP:GQ:MIN_DP:PL 0/0/0/0:8:8:8:0,9,21,42,315
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/
H A Dgvcf.basepairResolution.gvcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
108 20 10000000 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:52,0:52:99:0,120,1800
109 20 10000001 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:54,0:54:99:0,120,1800
110 20 10000002 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:50,0:50:99:0,120,1800
111 20 10000003 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:53,0:53:99:0,120,1800
112 20 10000004 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:50,0:50:99:0,120,1800
113 20 10000005 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:52,0:52:99:0,120,1800
149 20 10000041 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:43,1:44:93:0,93,1465
150 20 10000042 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:43,1:44:97:0,98,1488
151 20 10000043 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:41,1:42:88:0,89,1446
[all …]
H A DnewMQcalc.combined.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
427 20 10001437 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:57:0:57:0,0,0 ./.:42:0:42:0,0,0
1242 20 10006824 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:75:0:75:0,0,0 ./.:43:0:43:0,0,0
1405 20 10008030 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:91:0:91:0,0,0 ./.:47:0:47:0,0,0
1442 20 10008148 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:74:0:74:0,0,0 ./.:55:0:55:0,0,0
1489 20 10008759 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:55:0:55:0,0,0 ./.:42:0:42:0,0,0
1729 20 10010537 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:88:0:88:0,0,0 ./.:53:0:53:0,0,0
1874 20 10012023 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:69:0:69:0,0,0 ./.:54:0:54:0,0,0
2023 20 10012560 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:9:0:8:0,0,0 ./.:51:9:51:0,9,135
2027 20 10012571 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:11:0:11:0,0,0 ./.:51:0:51:0,0,0
[all …]
H A Dcombine.single.sample.pipeline.1.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
120 20 10000000 . T <NON_REF> . . END=10002217 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
122 20 10002282 . A <NON_REF> . . END=10003080 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
124 20 10003127 . C <NON_REF> . . END=10003373 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
128 20 10003449 . C <NON_REF> . . END=10004669 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
130 20 10004735 . C <NON_REF> . . END=10005674 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
134 20 10005724 . A <NON_REF> . . END=10011773 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
136 20 10011832 . A <NON_REF> . . END=10012698 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
142 20 10012756 . T <NON_REF> . . END=10014362 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
144 20 10014422 . G <NON_REF> . . END=10015485 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
[all …]
H A Dcombined.single.sample.pipeline.gatk3.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
38 20 10000265 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:3:0:3:0,0,34 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0
64 20 10003116 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:2:6:2:0,6,49 ./.:0:0:0:0,0,0 ./.:2:6:2:0,6,38
215 20 10017597 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:1:0:0:0,0,0
231 20 10018134 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:3:0:3:0,0,52 ./.:0:0:0:0,0,0
233 20 10018139 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:3:0:3:0,0,61 ./.:0:0:0:0,0,0
302 20 10023689 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:4:0:4:0,0,87 ./.:1:0:1:0,0,0
329 20 10024912 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:3:6:2:0,6,76
350 20 10026100 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:2:0:2:0,0,12 ./.:0:0:0:0,0,0
642 20 10040597 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0
[all …]
H A Dcombine.single.sample.pipeline.3.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
120 20 10000000 . T <NON_REF> . . END=10000202 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
124 20 10000282 . T <NON_REF> . . END=10001544 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
126 20 10001610 . A <NON_REF> . . END=10001691 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
128 20 10001740 . T <NON_REF> . . END=10002067 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
134 20 10002143 . T <NON_REF> . . END=10002338 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
136 20 10002410 . T <NON_REF> . . END=10002881 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
138 20 10002931 . T <NON_REF> . . END=10002989 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
144 20 10003117 . G <NON_REF> . . END=10003134 GT:DP:GQ:MIN_DP:PL 0/0:2:0:0:0,0,0
146 20 10003200 . C <NON_REF> . . END=10003318 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
[all …]
H A Dcombine.single.sample.pipeline.2.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
120 20 10000000 . T <NON_REF> . . END=10002833 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
122 20 10002851 . T <NON_REF> . . END=10009657 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
124 20 10009701 . A <NON_REF> . . END=10011133 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
126 20 10011179 . G <NON_REF> . . END=10012902 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
128 20 10012912 . A <NON_REF> . . END=10015462 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
143 20 10015618 . C <NON_REF> . . END=10016812 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
145 20 10016868 . T <NON_REF> . . END=10017156 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
147 20 10017235 . G <NON_REF> . . END=10017769 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
149 20 10017772 . T <NON_REF> . . END=10018069 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
[all …]
H A DtestUpdatePGT.gvcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
273 20 10001421 . G <NON_REF> . . END=10001421 GT:DP:GQ:MIN_DP:PL 0/0:44:9:44:0,9,135
287 20 10001437 . A <NON_REF> . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:44:0:44:0,0,0
355 20 10002450 . G <NON_REF> . . END=10002450 GT:DP:GQ:MIN_DP:PL 0/0:29:0:29:0,0,742
359 20 10002454 . G <NON_REF> . . END=10002454 GT:DP:GQ:MIN_DP:PL 0/0:27:4:27:0,4,763
861 20 10006824 . A <NON_REF> . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:40:0:40:0,0,0
985 20 10008030 . A <NON_REF> . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:54:0:54:0,0,0
1004 20 10008140 . T <NON_REF> . . END=10008145 GT:DP:GQ:MIN_DP:PL 0/0:51:0:50:0,0,0
1006 20 10008148 . A <NON_REF> . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:52:0:52:0,0,0
1050 20 10008759 . A <NON_REF> . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:23:0:23:0,0,0
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/ValidateVariants/
H A Dgvcf.basepairResolution.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
108 20 10000000 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:52,0:52:99:0,120,1800
109 20 10000001 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:54,0:54:99:0,120,1800
110 20 10000002 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:50,0:50:99:0,120,1800
111 20 10000003 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:53,0:53:99:0,120,1800
112 20 10000004 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:50,0:50:99:0,120,1800
113 20 10000005 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:52,0:52:99:0,120,1800
149 20 10000041 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:43,1:44:93:0,93,1465
150 20 10000042 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:43,1:44:97:0,98,1488
151 20 10000043 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:41,1:42:88:0,89,1446
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/
H A DnewMQcalc.combined.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
418 20 10001433 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:56:0:56:0,0,1779 ./.:42:6:41:0,6,90
420 20 10001435 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:55:0:55:0,0,1790 ./.:42:6:41:0,6,90
11202 20 10098311 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:2:6:2:0,6,80 ./.:39:0:33:0,0,0
11209 20 10098344 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:4:0:4:0,0,1 ./.:32:0:32:0,0,0
11217 20 10098357 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:3:3:3:0,3,45 ./.:23:6:23:0,6,90
11239 20 10098613 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./.:12:0:12:0,0,74
11243 20 10098617 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./.:14:0:14:0,0,6
11252 20 10098638 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:1:0:1:0,0,0 ./.:14:9:14:0,9,359
11257 20 10098647 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:1:0:1:0,0,0 ./.:16:0:16:0,0,228
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/
H A Dprod.chr20snippet.withRawMQ.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
102 chr20 19995071 . G <NON_REF> . . END=19995071 GT:DP:GQ:MIN_DP:PL 0/0:35:80:35:0,80,1087
104 chr20 19995074 . C <NON_REF> . . END=19995079 GT:DP:GQ:MIN_DP:PL 0/0:36:93:35:0,93,1395
105 chr20 19995080 . G <NON_REF> . . END=19995089 GT:DP:GQ:MIN_DP:PL 0/0:36:99:35:0,99,1485
135 chr20 19995242 . C <NON_REF> . . END=19995243 GT:DP:GQ:MIN_DP:PL 0/0:34:67:31:0,67,978
140 chr20 19995251 . G <NON_REF> . . END=19995251 GT:DP:GQ:MIN_DP:PL 0/0:33:50:33:0,50,968
144 chr20 19995261 . T <NON_REF> . . END=19995261 GT:DP:GQ:MIN_DP:PL 0/0:33:50:33:0,50,978
157 chr20 19995286 . C <NON_REF> . . END=19995286 GT:DP:GQ:MIN_DP:PL 0/0:33:74:33:0,74,997
161 chr20 19995290 . C <NON_REF> . . END=19995290 GT:DP:GQ:MIN_DP:PL 0/0:33:64:33:0,64,965
169 chr20 19995312 . A <NON_REF> . . END=19995314 GT:DP:GQ:MIN_DP:PL 0/0:31:84:28:0,84,973
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/
H A Dsample1.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
39 chr20 251378 . T <NON_REF> . . END=251378 GT:DP:GQ:MIN_DP:PL 0/0:18:5:18:0,5,467
51 chr20 251418 . A <NON_REF> . . END=251418 GT:DP:GQ:MIN_DP:PL 0/0:25:6:25:0,6,710
53 chr20 251422 . T <NON_REF> . . END=251422 GT:DP:GQ:MIN_DP:PL 0/0:25:6:25:0,6,720
67 chr20 252041 . T <NON_REF> . . END=252041 GT:DP:GQ:MIN_DP:PL 0/0:26:4:26:0,4,665
93 chr20 252902 . T <NON_REF> . . END=252902 GT:DP:GQ:MIN_DP:PL 0/0:27:3:27:0,3,662
352 chr20 262182 . C <NON_REF> . . END=262182 GT:DP:GQ:MIN_DP:PL 0/0:7:6:7:0,6,164
510 chr20 278937 . A <NON_REF> . . END=278943 GT:DP:GQ:MIN_DP:PL 0/0:7:7:7:0,7,135
512 chr20 278953 . A <NON_REF> . . END=278959 GT:DP:GQ:MIN_DP:PL 0/0:7:9:7:0,9,135
517 chr20 278982 . G <NON_REF> . . END=278984 GT:DP:GQ:MIN_DP:PL 0/0:6:3:6:0,3,139
[all …]
H A Dsample2.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
46 chr20 251411 . T <NON_REF> . . END=251411 GT:DP:GQ:MIN_DP:PL 0/0:25:6:25:0,6,700
48 chr20 251418 . A <NON_REF> . . END=251418 GT:DP:GQ:MIN_DP:PL 0/0:26:9:26:0,9,745
63 chr20 252896 . G <NON_REF> . . END=252896 GT:DP:GQ:MIN_DP:PL 0/0:26:8:26:0,8,693
65 chr20 252904 . A <NON_REF> . . END=252904 GT:DP:GQ:MIN_DP:PL 0/0:24:4:24:0,4,587
67 chr20 252908 . C <NON_REF> . . END=252908 GT:DP:GQ:MIN_DP:PL 0/0:25:5:25:0,5,679
69 chr20 252920 . T <NON_REF> . . END=252920 GT:DP:GQ:MIN_DP:PL 0/0:18:5:18:0,5,477
154 chr20 255805 . A <NON_REF> . . END=255817 GT:DP:GQ:MIN_DP:PL 0/0:11:6:9:0,6,90
205 chr20 257152 . C <NON_REF> . . END=257164 GT:DP:GQ:MIN_DP:PL 0/0:34:3:34:0,3,45
206 chr20 257173 . T <NON_REF> . . END=257174 GT:DP:GQ:MIN_DP:PL 0/0:36:3:36:0,3,45
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/
H A Dexpected.testGVCFMode.gatk3.5.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
131 20 10001437 . A <NON_REF> . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:57:0:57:0,0,0
265 20 10006824 . A <NON_REF> . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0
284 20 10008030 . A <NON_REF> . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:91:0:91:0,0,0
298 20 10008148 . A <NON_REF> . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:74:0:74:0,0,0
318 20 10008759 . A <NON_REF> . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0
338 20 10008950 . A <NON_REF> . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:48:0:48:0,0,0
586 20 10012556 . T <NON_REF> . . END=10012557 GT:DP:GQ:MIN_DP:PL 0/0:9:6:9:0,6,90
587 20 10012558 . C <NON_REF> . . END=10012558 GT:DP:GQ:MIN_DP:PL 0/0:9:3:9:0,3,45
588 20 10012559 . C <NON_REF> . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:0:8:0,0,0
[all …]
H A Dexpected.testGVCFMode.3.8-4-g7b0250253f.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
135 20 10001437 . A <NON_REF> . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:57:0:57:0,0,0
269 20 10006824 . A <NON_REF> . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0
288 20 10008030 . A <NON_REF> . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:91:0:91:0,0,0
302 20 10008148 . A <NON_REF> . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:74:0:74:0,0,0
322 20 10008759 . A <NON_REF> . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0
342 20 10008950 . A <NON_REF> . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:48:0:48:0,0,0
588 20 10012556 . T <NON_REF> . . END=10012557 GT:DP:GQ:MIN_DP:PL 0/0:9:6:9:0,6,90
589 20 10012558 . C <NON_REF> . . END=10012558 GT:DP:GQ:MIN_DP:PL 0/0:9:3:9:0,3,45
590 20 10012559 . C <NON_REF> . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:0:8:0,0,0
[all …]
H A Dexpected.testGVCFMode.gatk4.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
111 20 10001427 . T <NON_REF> . . END=10001427 GT:DP:GQ:MIN_DP:PL 0/0:53:5:53:0,5,1899
113 20 10001430 . G <NON_REF> . . END=10001431 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1743
155 20 10002478 . A <NON_REF> . . END=10002481 GT:DP:GQ:MIN_DP:PL 0/0:56:0:50:0,0,731
614 20 10015548 . G <NON_REF> . . END=10015565 GT:DP:GQ:MIN_DP:PL 0/0:11:0:6:0,0,0
615 20 10015566 . G <NON_REF> . . END=10015580 GT:DP:GQ:MIN_DP:PL 0/0:5:3:5:0,3,45
616 20 10015581 . G <NON_REF> . . END=10015598 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,69
1231 20 10098344 . A <NON_REF> . . END=10098344 GT:DP:GQ:MIN_DP:PL 0/0:4:0:4:0,0,1
1234 20 10098361 . T <NON_REF> . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
1236 20 10098455 . A <NON_REF> . . END=10098551 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
[all …]
H A Dexpected.testGVCFMode.gatk3.5.alleleSpecific.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
142 20 10001437 . A <NON_REF> . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:57:0:57:0,0,0
276 20 10006824 . A <NON_REF> . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0
295 20 10008030 . A <NON_REF> . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:91:0:91:0,0,0
309 20 10008148 . A <NON_REF> . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:74:0:74:0,0,0
329 20 10008759 . A <NON_REF> . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0
597 20 10012556 . T <NON_REF> . . END=10012557 GT:DP:GQ:MIN_DP:PL 0/0:9:6:9:0,6,90
598 20 10012558 . C <NON_REF> . . END=10012558 GT:DP:GQ:MIN_DP:PL 0/0:9:3:9:0,3,45
599 20 10012559 . C <NON_REF> . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:0:8:0,0,0
741 20 10015548 . G <NON_REF> . . END=10015565 GT:DP:GQ:MIN_DP:PL 0/0:11:0:6:0,0,0
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/
H A Dexpected.testGenomicsDBImportWithNonDiploidData.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
205 20 10001427 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:53:5:53:0,5,1899 ./.
209 20 10001433 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:56:0:56:0,0,1779 ./.
211 20 10001435 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:55:0:55:0,0,1790 ./.
238 20 10002457 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:52:0:52:0,0,1572 ./.
250 20 10002482 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:46:3:46:0,3,1461 ./.
591 20 10012549 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:6:1:6:0,1,186 ./.
743 20 10015599 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:3:9:3:0,9,109 ./.
1490 20 10098344 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:4:0:4:0,0,1 ./.
1505 20 10098713 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:8:0:8:0,0,262 ./.
[all …]
H A Dexpected.testGVCFMode.gatk4.g.vcf6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
112 20 10001427 . T <NON_REF> . . END=10001427 GT:DP:GQ:MIN_DP:PL 0/0:53:5:53:0,5,1899
114 20 10001430 . G <NON_REF> . . END=10001431 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1743
156 20 10002478 . A <NON_REF> . . END=10002481 GT:DP:GQ:MIN_DP:PL 0/0:56:0:50:0,0,731
614 20 10015548 . G <NON_REF> . . END=10015565 GT:DP:GQ:MIN_DP:PL 0/0:11:0:6:0,0,0
615 20 10015566 . G <NON_REF> . . END=10015580 GT:DP:GQ:MIN_DP:PL 0/0:5:3:5:0,3,45
616 20 10015581 . G <NON_REF> . . END=10015598 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,69
1231 20 10098344 . A <NON_REF> . . END=10098344 GT:DP:GQ:MIN_DP:PL 0/0:4:0:4:0,0,1
1234 20 10098361 . T <NON_REF> . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
1236 20 10098455 . A <NON_REF> . . END=10098551 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
[all …]

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