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Test expected updated
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‎src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf‎

Lines changed: 36 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -4827,13 +4827,13 @@ chr9 81158612 . A <NON_REF> . . END=81158614 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,2
48274827
chr9 81158615 . A <NON_REF> . . END=81158615 GT:DP:GQ:MIN_DP:PL 0/0:10:24:10:0,24,360
48284828
chr9 81158616 . T <NON_REF> . . END=81158616 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,27,405
48294829
chr9 81158617 . A <NON_REF> . . END=81158617 GT:DP:GQ:MIN_DP:PL 0/0:11:9:11:0,9,399
4830-
chr9 81158618 . T A,<NON_REF> 4.66 . ASSEMBLED_HAPS=51;BaseQRankSum=-1.645;DP=11;ExcessHet=0.0000;FILTERED_HAPS=40;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=39600,11;ReadPosRankSum=-0.842;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:9,1,0:10:12:12,0,351,39,354,393:6,3,1,0
4830+
chr9 81158618 . T A,<NON_REF> 4.66 . ASSEMBLED_HAPS=51;BaseQRankSum=-1.645;DP=11;ExcessHet=0.0000;FILTERED_HAPS=34;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=39600,11;ReadPosRankSum=-0.842;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:9,1,0:10:12:12,0,356,39,359,398:6,3,1,0
48314831
chr9 81158619 . G <NON_REF> . . END=81158621 GT:DP:GQ:MIN_DP:PL 0/0:9:27:9:0,27,377
48324832
chr9 81158622 . C <NON_REF> . . END=81158625 GT:DP:GQ:MIN_DP:PL 0/0:10:30:10:0,30,436
48334833
chr9 81158626 . T <NON_REF> . . END=81158635 GT:DP:GQ:MIN_DP:PL 0/0:12:36:12:0,36,415
48344834
chr9 81158636 . C <NON_REF> . . END=81158636 GT:DP:GQ:MIN_DP:PL 0/0:13:39:13:0,39,481
48354835
chr9 81158637 . T <NON_REF> . . END=81158647 GT:DP:GQ:MIN_DP:PL 0/0:12:33:11:0,33,492
4836-
chr9 81158648 . G <NON_REF> . . END=81158648 GT:DP:GQ:MIN_DP:PL 0/0:11:27:11:0,27,405
4836+
chr9 81158648 . G GA,<NON_REF> 0.01 . ASSEMBLED_HAPS=51;BaseQRankSum=0.000;DP=13;ExcessHet=0.0000;FILTERED_HAPS=34;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=46800,13;ReadPosRankSum=-0.447;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:10,2,0:12:1:1,0,220,30,225,255:6,4,2,0
48374837
chr9 81158649 . A <NON_REF> . . END=81158655 GT:DP:GQ:MIN_DP:PL 0/0:11:33:11:0,33,368
48384838
chr9 81158656 . A <NON_REF> . . END=81158656 GT:DP:GQ:MIN_DP:PL 0/0:12:21:12:0,21,461
48394839
chr9 81158657 . C <NON_REF> . . END=81158660 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495
@@ -4845,10 +4845,10 @@ chr9 81158672 . C <NON_REF> . . END=81158673 GT:DP:GQ:MIN_DP:PL 0/0:15:45:15:0,4
48454845
chr9 81158674 . A <NON_REF> . . END=81158678 GT:DP:GQ:MIN_DP:PL 0/0:15:42:15:0,42,630
48464846
chr9 81158679 . C <NON_REF> . . END=81158687 GT:DP:GQ:MIN_DP:PL 0/0:14:39:14:0,39,585
48474847
chr9 81158688 . T <NON_REF> . . END=81158689 GT:DP:GQ:MIN_DP:PL 0/0:14:36:13:0,36,540
4848-
chr9 81158690 . C CT,<NON_REF> 374.02 . ASSEMBLED_HAPS=51;DP=14;ExcessHet=0.0000;FILTERED_HAPS=40;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=50400,14 GT:AD:DP:GQ:PL:SB 1/1:0,13,0:13:39:388,39,0,388,39,388:0,0,10,3
4848+
chr9 81158690 . C CT,<NON_REF> 374.02 . ASSEMBLED_HAPS=51;DP=14;ExcessHet=0.0000;FILTERED_HAPS=34;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=50400,14 GT:AD:DP:GQ:PL:SB 1/1:0,13,0:13:39:388,39,0,388,39,388:0,0,10,3
48494849
chr9 81158691 . G <NON_REF> . . END=81158693 GT:DP:GQ:MIN_DP:PL 0/0:13:39:13:0,39,549
48504850
chr9 81158694 . T <NON_REF> . . END=81158711 GT:DP:GQ:MIN_DP:PL 0/0:14:42:14:0,42,553
4851-
chr9 81158712 . A G,<NON_REF> 265.64 . ASSEMBLED_HAPS=51;BaseQRankSum=0.674;DP=14;ExcessHet=0.0000;FILTERED_HAPS=40;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=50400,14;ReadPosRankSum=-1.190 GT:AD:DP:GQ:PL:SB 0/1:7,7,0:14:99:273,0,268,294,289,583:7,0,4,3
4851+
chr9 81158712 . A G,<NON_REF> 265.64 . ASSEMBLED_HAPS=51;BaseQRankSum=0.674;DP=14;ExcessHet=0.0000;FILTERED_HAPS=34;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=50400,14;ReadPosRankSum=-1.190 GT:AD:DP:GQ:PL:SB 0/1:7,7,0:14:99:273,0,273,294,294,588:7,0,4,3
48524852
chr9 81158713 . A <NON_REF> . . END=81158713 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,48,714
48534853
chr9 81158714 . C <NON_REF> . . END=81158714 GT:DP:GQ:MIN_DP:PL 0/0:16:45:16:0,45,675
48544854
chr9 81158715 . T <NON_REF> . . END=81158717 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,48,681
@@ -4935,31 +4935,32 @@ chr9 81159092 . G <NON_REF> . . END=81159092 GT:DP:GQ:MIN_DP:PL 0/0:12:24:12:0,2
49354935
chr9 81159093 . A <NON_REF> . . END=81159093 GT:DP:GQ:MIN_DP:PL 0/0:12:22:12:0,22,454
49364936
chr9 81159094 . C <NON_REF> . . END=81159095 GT:DP:GQ:MIN_DP:PL 0/0:11:24:10:0,24,360
49374937
chr9 81159096 . C <NON_REF> . . END=81159096 GT:DP:GQ:MIN_DP:PL 0/0:10:27:10:0,27,405
4938-
chr9 81159097 . T C,<NON_REF> 276.02 . ASSEMBLED_HAPS=46;DP=9;ExcessHet=0.0000;FILTERED_HAPS=43;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=32400,9 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,7,0:7:21:0|1:81159097_T_C:290,21,0,290,21,290:81159097:0,0,4,3
4938+
chr9 81159097 . T C,<NON_REF> 310.04 . ASSEMBLED_HAPS=46;DP=9;ExcessHet=0.0000;FILTERED_HAPS=41;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=32400,9 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,8,0:8:24:0|1:81159097_T_C:324,24,0,324,24,324:81159097:0,0,5,3
49394939
chr9 81159098 . G <NON_REF> . . END=81159099 GT:DP:GQ:MIN_DP:PL 0/0:8:18:8:0,18,270
49404940
chr9 81159100 . C <NON_REF> . . END=81159101 GT:DP:GQ:MIN_DP:PL 0/0:8:12:8:0,12,180
4941-
chr9 81159102 . C CA,<NON_REF> 275.98 . ASSEMBLED_HAPS=46;DP=9;ExcessHet=0.0000;FILTERED_HAPS=43;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=32400,9 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,7,0:7:21:0|1:81159097_T_C:290,21,0,290,21,290:81159097:0,0,4,3
4942-
chr9 81159103 . A <NON_REF> . . END=81159103 GT:DP:GQ:MIN_DP:PL 0/0:6:6:6:0,6,79
4943-
chr9 81159104 . A <NON_REF> . . END=81159104 GT:DP:GQ:MIN_DP:PL 0/0:6:7:6:0,7,107
4944-
chr9 81159105 . A <NON_REF> . . END=81159106 GT:DP:GQ:MIN_DP:PL 0/0:6:12:6:0,12,180
4945-
chr9 81159107 . A <NON_REF> . . END=81159107 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,99
4946-
chr9 81159108 . A <NON_REF> . . END=81159109 GT:DP:GQ:MIN_DP:PL 0/0:6:5:6:0,5,81
4947-
chr9 81159110 . A <NON_REF> . . END=81159110 GT:DP:GQ:MIN_DP:PL 0/0:5:2:5:0,2,44
4948-
chr9 81159111 . A <NON_REF> . . END=81159121 GT:DP:GQ:MIN_DP:PL 0/0:5:0:4:0,0,1
4949-
chr9 81159122 . A <NON_REF> . . END=81159123 GT:DP:GQ:MIN_DP:PL 0/0:5:15:5:0,15,147
4950-
chr9 81159124 . A <NON_REF> . . END=81159124 GT:DP:GQ:MIN_DP:PL 0/0:6:18:6:0,18,162
4951-
chr9 81159125 . A <NON_REF> . . END=81159126 GT:DP:GQ:MIN_DP:PL 0/0:6:15:5:0,15,196
4952-
chr9 81159127 . T <NON_REF> . . END=81159127 GT:DP:GQ:MIN_DP:PL 0/0:5:12:5:0,12,180
4953-
chr9 81159128 . A <NON_REF> . . END=81159129 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,44
4941+
chr9 81159102 . C CA,<NON_REF> 310 . ASSEMBLED_HAPS=46;DP=9;ExcessHet=0.0000;FILTERED_HAPS=41;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=32400,9 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,8,0:8:24:0|1:81159097_T_C:324,24,0,324,24,324:81159097:0,0,5,3
4942+
chr9 81159103 . A <NON_REF> . . END=81159103 GT:DP:GQ:MIN_DP:PL 0/0:6:6:6:0,6,90
4943+
chr9 81159104 . A <NON_REF> . . END=81159112 GT:DP:GQ:MIN_DP:PL 0/0:6:0:4:0,0,0
4944+
chr9 81159113 . A <NON_REF> . . END=81159113 GT:DP:GQ:MIN_DP:PL 0/0:4:12:4:0,12,95
4945+
chr9 81159114 . A <NON_REF> . . END=81159115 GT:DP:GQ:MIN_DP:PL 0/0:5:0:5:0,0,53
4946+
chr9 81159116 . A <NON_REF> . . END=81159118 GT:DP:GQ:MIN_DP:PL 0/0:5:15:5:0,15,102
4947+
chr9 81159119 . A <NON_REF> . . END=81159120 GT:DP:GQ:MIN_DP:PL 0/0:5:12:4:0,12,70
4948+
chr9 81159121 . A <NON_REF> . . END=81159121 GT:DP:GQ:MIN_DP:PL 0/0:5:14:5:0,14,117
4949+
chr9 81159122 . A <NON_REF> . . END=81159123 GT:DP:GQ:MIN_DP:PL 0/0:5:15:5:0,15,148
4950+
chr9 81159124 . A <NON_REF> . . END=81159124 GT:DP:GQ:MIN_DP:PL 0/0:6:18:6:0,18,161
4951+
chr9 81159125 . A <NON_REF> . . END=81159125 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,38
4952+
chr9 81159126 . T <NON_REF> . . END=81159126 GT:DP:GQ:MIN_DP:PL 0/0:5:12:5:0,12,180
4953+
chr9 81159127 . T <NON_REF> . . END=81159129 GT:DP:GQ:MIN_DP:PL 0/0:6:0:5:0,0,44
49544954
chr9 81159130 . A <NON_REF> . . END=81159132 GT:DP:GQ:MIN_DP:PL 0/0:6:18:6:0,18,154
49554955
chr9 81159133 . A <NON_REF> . . END=81159134 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,48
49564956
chr9 81159135 . A <NON_REF> . . END=81159136 GT:DP:GQ:MIN_DP:PL 0/0:5:15:5:0,15,134
4957-
chr9 81159137 . C <NON_REF> . . END=81159138 GT:DP:GQ:MIN_DP:PL 0/0:6:0:5:0,0,27
4958-
chr9 81159139 . A <NON_REF> . . END=81159139 GT:DP:GQ:MIN_DP:PL 0/0:6:4:6:0,4,127
4957+
chr9 81159137 . C A,<NON_REF> 16.63 . ASSEMBLED_HAPS=46;BaseQRankSum=-1.150;DP=6;ExcessHet=0.0000;FILTERED_HAPS=41;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=21600,6;ReadPosRankSum=-0.524;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:3,2,0:5:24:0|1:81159097_T_C:24,0,91,33,95,129:81159097:1,2,2,0
4958+
chr9 81159138 . A C,<NON_REF> 16.63 . ASSEMBLED_HAPS=46;BaseQRankSum=0.000;DP=6;ExcessHet=0.0000;FILTERED_HAPS=41;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=21600,6;ReadPosRankSum=-0.524;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:3,2,0:5:24:0|1:81159097_T_C:24,0,91,33,95,129:81159097:1,2,2,0
4959+
chr9 81159139 . A <NON_REF> . . END=81159139 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,110
49594960
chr9 81159140 . A <NON_REF> . . END=81159140 GT:DP:GQ:MIN_DP:PL 0/0:6:18:6:0,18,168
49604961
chr9 81159141 . A <NON_REF> . . END=81159141 GT:DP:GQ:MIN_DP:PL 0/0:5:14:5:0,14,133
49614962
chr9 81159142 . A <NON_REF> . . END=81159142 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,89
4962-
chr9 81159143 . G T,<NON_REF> 19.64 . ASSEMBLED_HAPS=46;BaseQRankSum=0.000;DP=9;ExcessHet=0.0000;FILTERED_HAPS=43;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=32400,9;ReadPosRankSum=-0.967;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:5,1,0:6:27:0|1:81159097_T_C:27,0,164,42,167,209:81159097:2,3,1,0
4963+
chr9 81159143 . G T,<NON_REF> 16.63 . ASSEMBLED_HAPS=46;BaseQRankSum=0.000;DP=9;ExcessHet=0.0000;FILTERED_HAPS=41;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=32400,9;ReadPosRankSum=-1.068;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:6,1,0:7:24:0|1:81159097_T_C:24,0,199,42,202,244:81159097:3,3,1,0
49634964
chr9 81159144 . A <NON_REF> . . END=81159145 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,257
49644965
chr9 81159146 . A <NON_REF> . . END=81159151 GT:DP:GQ:MIN_DP:PL 0/0:9:27:9:0,27,370
49654966
chr9 81159152 . A <NON_REF> . . END=81159153 GT:DP:GQ:MIN_DP:PL 0/0:9:24:8:0,24,348
@@ -5431,9 +5432,9 @@ chr9 81162397 . C <NON_REF> . . END=81162397 GT:DP:GQ:MIN_DP:PL 0/0:44:98:44:0,9
54315432
chr9 81162398 . A <NON_REF> . . END=81162403 GT:DP:GQ:MIN_DP:PL 0/0:45:99:44:0,107,1800
54325433
chr9 81162404 . A <NON_REF> . . END=81162404 GT:DP:GQ:MIN_DP:PL 0/0:45:91:45:0,91,1882
54335434
chr9 81162405 . C <NON_REF> . . END=81162430 GT:DP:GQ:MIN_DP:PL 0/0:47:99:45:0,120,1800
5434-
chr9 81162431 . G C,<NON_REF> 0 . ASSEMBLED_HAPS=14;BaseQRankSum=-1.126;DP=48;ExcessHet=0.0000;FILTERED_HAPS=11;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=172800,48;ReadPosRankSum=-1.175;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:44,3,0:47:45:0|1:81162431_G_C:0,45,85,132,1847,172:81162431:23,21,0,3
5435+
chr9 81162431 . G C,<NON_REF> 0 . ASSEMBLED_HAPS=14;BaseQRankSum=-1.126;DP=48;ExcessHet=0.0000;FILTERED_HAPS=11;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=172800,48;ReadPosRankSum=-1.175;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:44,3,0:47:45:0|1:81162431_G_C:0,45,1838,132,1847,1934:81162431:23,21,0,3
54355436
chr9 81162432 . G <NON_REF> . . END=81162432 GT:DP:GQ:MIN_DP:PL 0/0:46:99:46:0,120,1800
5436-
chr9 81162433 . A AG,<NON_REF> 0 . ASSEMBLED_HAPS=14;BaseQRankSum=-2.125;DP=48;ExcessHet=0.0000;FILTERED_HAPS=11;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=172800,48;ReadPosRankSum=-1.258;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:43,4,0:47:16:0|1:81162431_G_C:0,16,56,125,948,165:81162431:23,20,0,4
5437+
chr9 81162433 . A AG,<NON_REF> 0 . ASSEMBLED_HAPS=14;BaseQRankSum=-2.125;DP=48;ExcessHet=0.0000;FILTERED_HAPS=11;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=172800,48;ReadPosRankSum=-1.258;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:43,4,0:47:15:0|1:81162431_G_C:0,15,935,124,947,1056:81162431:23,20,0,4
54375438
chr9 81162434 . G <NON_REF> . . END=81162469 GT:DP:GQ:MIN_DP:PL 0/0:45:99:44:0,104,1800
54385439
chr9 81162470 . A <NON_REF> . . END=81162470 GT:DP:GQ:MIN_DP:PL 0/0:44:94:44:0,94,1853
54395440
chr9 81162471 . G <NON_REF> . . END=81162477 GT:DP:GQ:MIN_DP:PL 0/0:48:99:44:0,113,1776
@@ -6031,13 +6032,13 @@ chr9 81167733 . A <NON_REF> . . END=81167733 GT:DP:GQ:MIN_DP:PL 0/0:37:67:37:0,6
60316032
chr9 81167734 . T <NON_REF> . . END=81167735 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,111,1527
60326033
chr9 81167736 . T <NON_REF> . . END=81167736 GT:DP:GQ:MIN_DP:PL 0/0:37:90:37:0,90,1461
60336034
chr9 81167737 . A <NON_REF> . . END=81167740 GT:DP:GQ:MIN_DP:PL 0/0:38:99:35:0,105,1439
6034-
chr9 81167741 . GAAAA G,<NON_REF> 0.04 . ASSEMBLED_HAPS=7;BaseQRankSum=0.500;DP=32;ExcessHet=0.0000;FILTERED_HAPS=4;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-0.611;RAW_MQandDP=110827,32;ReadPosRankSum=-2.151;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:26,4,0:30:3:0|1:81167741_GAAAA_G:3,0,40,81,997,121:81167741:12,14,3,1
6035+
chr9 81167741 . GAAAA G,<NON_REF> 0.04 . ASSEMBLED_HAPS=7;BaseQRankSum=0.500;DP=32;ExcessHet=0.0000;FILTERED_HAPS=4;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-0.611;RAW_MQandDP=110827,32;ReadPosRankSum=-2.151;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:26,4,0:30:3:0|1:81167741_GAAAA_G:3,0,901,81,997,993:81167741:12,14,3,1
60356036
chr9 81167746 . A <NON_REF> . . END=81167746 GT:DP:GQ:MIN_DP:PL 0/0:31:54:31:0,54,1133
60366037
chr9 81167747 . A <NON_REF> . . END=81167747 GT:DP:GQ:MIN_DP:PL 0/0:30:52:30:0,52,1164
60376038
chr9 81167748 . A <NON_REF> . . END=81167750 GT:DP:GQ:MIN_DP:PL 0/0:30:84:30:0,84,1260
60386039
chr9 81167751 . A <NON_REF> . . END=81167751 GT:DP:GQ:MIN_DP:PL 0/0:23:65:23:0,65,316
60396040
chr9 81167752 . C <NON_REF> . . END=81167756 GT:DP:GQ:MIN_DP:PL 0/0:30:87:29:0,87,1223
6040-
chr9 81167757 . CA C,<NON_REF> 20.60 . ASSEMBLED_HAPS=7;BaseQRankSum=0.648;DP=30;ExcessHet=0.0000;FILTERED_HAPS=4;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.402;RAW_MQandDP=102731,30;ReadPosRankSum=-1.994;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:25,4,0:29:28:0|1:81167741_GAAAA_G:28,0,40,103,634,143:81167741:11,14,3,1
6041+
chr9 81167757 . CA C,<NON_REF> 20.60 . ASSEMBLED_HAPS=7;BaseQRankSum=0.648;DP=30;ExcessHet=0.0000;FILTERED_HAPS=4;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.402;RAW_MQandDP=102731,30;ReadPosRankSum=-1.994;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:25,4,0:29:28:0|1:81167741_GAAAA_G:28,0,569,103,634,684:81167741:11,14,3,1
60416042
chr9 81167759 . A <NON_REF> . . END=81167776 GT:DP:GQ:MIN_DP:PL 0/0:39:99:34:0,102,1198
60426043
chr9 81167777 . T <NON_REF> . . END=81167777 GT:DP:GQ:MIN_DP:PL 0/0:40:58:40:0,58,1639
60436044
chr9 81167778 . G <NON_REF> . . END=81167795 GT:DP:GQ:MIN_DP:PL 0/0:40:99:38:0,101,1445
@@ -6593,26 +6594,24 @@ chr9 81171246 . A <NON_REF> . . END=81171249 GT:DP:GQ:MIN_DP:PL 0/0:18:51:18:0,5
65936594
chr9 81171250 . G <NON_REF> . . END=81171250 GT:DP:GQ:MIN_DP:PL 0/0:17:45:17:0,45,675
65946595
chr9 81171251 . T <NON_REF> . . END=81171251 GT:DP:GQ:MIN_DP:PL 0/0:18:9:18:0,9,716
65956596
chr9 81171252 . A <NON_REF> . . END=81171253 GT:DP:GQ:MIN_DP:PL 0/0:17:45:17:0,45,675
6596-
chr9 81171254 . TA T,<NON_REF> 37.60 . ASSEMBLED_HAPS=41;BaseQRankSum=0.000;DP=19;ExcessHet=0.0000;FILTERED_HAPS=31;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.588;RAW_MQandDP=58756,19;ReadPosRankSum=-1.025;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:13,2,0:15:45:45,0,540,84,546,630:10,3,2,0
6597-
chr9 81171255 . AGTGTGTGTGTGTGT A,*,<NON_REF> 128 . ASSEMBLED_HAPS=41;BaseQRankSum=0.000;DP=20;ExcessHet=0.0000;FILTERED_HAPS=31;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.967;RAW_MQandDP=62356,20;ReadPosRankSum=0.241;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:3,4,2,0:9:60:156,0,141,99,60,471,186,171,480,591:3,0,3,3
6597+
chr9 81171254 . TA T,<NON_REF> 34.60 . ASSEMBLED_HAPS=41;BaseQRankSum=0.000;DP=19;ExcessHet=0.0000;FILTERED_HAPS=21;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.567;RAW_MQandDP=58756,19;ReadPosRankSum=-1.116;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:14,2,0:16:42:42,0,582,84,588,672:11,3,2,0
6598+
chr9 81171255 . AGTGTGTGTGTGTGT A,*,<NON_REF> 170 . ASSEMBLED_HAPS=41;BaseQRankSum=0.000;DP=20;ExcessHet=0.0000;FILTERED_HAPS=21;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=1.036;RAW_MQandDP=62356,20;ReadPosRankSum=0.536;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:3,5,2,0:10:60:198,0,138,141,60,513,228,171,522,633:3,0,4,3
65986599
chr9 81171270 . G <NON_REF> . . END=81171271 GT:DP:GQ:MIN_DP:PL 0/0:16:18:16:0,18,270
65996600
chr9 81171272 . G <NON_REF> . . END=81171275 GT:DP:GQ:MIN_DP:PL 0/0:16:15:13:0,15,225
6600-
chr9 81171276 . G <NON_REF> . . END=81171277 GT:DP:GQ:MIN_DP:PL 0/0:11:18:10:0,18,270
6601-
chr9 81171278 . G <NON_REF> . . END=81171278 GT:DP:GQ:MIN_DP:PL 0/0:10:15:10:0,15,225
6602-
chr9 81171279 . T <NON_REF> . . END=81171280 GT:DP:GQ:MIN_DP:PL 0/0:11:0:10:0,0,341
6603-
chr9 81171281 . T <NON_REF> . . END=81171282 GT:DP:GQ:MIN_DP:PL 0/0:12:1:12:0,1,406
6604-
chr9 81171283 . T <NON_REF> . . END=81171288 GT:DP:GQ:MIN_DP:PL 0/0:8:0:8:0,0,257
6605-
chr9 81171289 . T G,<NON_REF> 28.64 . ASSEMBLED_HAPS=41;BaseQRankSum=0.319;DP=11;ExcessHet=0.0000;FILTERED_HAPS=31;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=32400,11;ReadPosRankSum=-0.464 GT:AD:DP:GQ:PL:SB 0/1:6,2,0:8:36:36,0,216,54,222,276:1,5,1,1
6606-
chr9 81171290 . G <NON_REF> . . END=81171292 GT:DP:GQ:MIN_DP:PL 0/0:8:0:8:0,0,254
6601+
chr9 81171276 . G <NON_REF> . . END=81171279 GT:DP:GQ:MIN_DP:PL 0/0:11:18:10:0,18,270
6602+
chr9 81171280 . G <NON_REF> . . END=81171288 GT:DP:GQ:MIN_DP:PL 0/0:11:24:8:0,24,319
6603+
chr9 81171289 . T G,<NON_REF> 25.64 . ASSEMBLED_HAPS=41;BaseQRankSum=0.282;DP=11;ExcessHet=0.0000;FILTERED_HAPS=21;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=32400,11;ReadPosRankSum=-0.674 GT:AD:DP:GQ:PL:SB 0/1:7,2,0:9:33:33,0,258,54,264,318:2,5,1,1
6604+
chr9 81171290 . G <NON_REF> . . END=81171290 GT:DP:GQ:MIN_DP:PL 0/0:7:21:7:0,21,310
6605+
chr9 81171291 . G <NON_REF> . . END=81171292 GT:DP:GQ:MIN_DP:PL 0/0:8:0:8:0,0,254
66076606
chr9 81171293 . A <NON_REF> . . END=81171296 GT:DP:GQ:MIN_DP:PL 0/0:9:24:8:0,24,302
66086607
chr9 81171297 . G <NON_REF> . . END=81171299 GT:DP:GQ:MIN_DP:PL 0/0:10:27:10:0,27,405
66096608
chr9 81171300 . A <NON_REF> . . END=81171302 GT:DP:GQ:MIN_DP:PL 0/0:11:30:11:0,30,450
66106609
chr9 81171303 . A <NON_REF> . . END=81171304 GT:DP:GQ:MIN_DP:PL 0/0:12:33:12:0,33,495
66116610
chr9 81171305 . T <NON_REF> . . END=81171305 GT:DP:GQ:MIN_DP:PL 0/0:13:36:13:0,36,540
66126611
chr9 81171306 . G <NON_REF> . . END=81171311 GT:DP:GQ:MIN_DP:PL 0/0:14:39:13:0,39,553
6613-
chr9 81171312 . C <NON_REF> . . END=81171312 GT:DP:GQ:MIN_DP:PL 0/0:14:20:14:0,20,560
6612+
chr9 81171312 . C T,<NON_REF> 0.05 . ASSEMBLED_HAPS=41;BaseQRankSum=-3.328;DP=16;ExcessHet=0.0000;FILTERED_HAPS=21;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=50400,16;ReadPosRankSum=1.490;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:13,1,0:14:3:3,0,543,42,546,588:5,8,1,0
66146613
chr9 81171313 . A <NON_REF> . . END=81171314 GT:DP:GQ:MIN_DP:PL 0/0:14:36:14:0,36,540
6615-
chr9 81171315 . C <NON_REF> . . END=81171315 GT:DP:GQ:MIN_DP:PL 0/0:14:13:14:0,13,553
6614+
chr9 81171315 . C G,<NON_REF> 0.05 . ASSEMBLED_HAPS=41;BaseQRankSum=-3.328;DP=16;ExcessHet=0.0000;FILTERED_HAPS=21;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQandDP=50400,16;ReadPosRankSum=1.490;SUSP_NOISY_ADJACENT_TP_VARIANT GT:AD:DP:GQ:PL:SB 0/1:13,1,0:14:3:3,0,543,42,546,588:5,8,1,0
66166615
chr9 81171316 . T <NON_REF> . . END=81171317 GT:DP:GQ:MIN_DP:PL 0/0:14:36:14:0,36,540
66176616
chr9 81171318 . G <NON_REF> . . END=81171318 GT:DP:GQ:MIN_DP:PL 0/0:14:26:14:0,26,554
66186617
chr9 81171319 . G <NON_REF> . . END=81171320 GT:DP:GQ:MIN_DP:PL 0/0:14:39:13:0,39,570
@@ -6630,7 +6629,7 @@ chr9 81171375 . T <NON_REF> . . END=81171376 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,4
66306629
chr9 81171377 . T <NON_REF> . . END=81171398 GT:DP:GQ:MIN_DP:PL 0/0:16:45:15:0,45,672
66316630
chr9 81171399 . G <NON_REF> . . END=81171399 GT:DP:GQ:MIN_DP:PL 0/0:14:42:14:0,42,612
66326631
chr9 81171400 . A <NON_REF> . . END=81171415 GT:DP:GQ:MIN_DP:PL 0/0:16:48:16:0,48,646
6633-
chr9 81171416 . C T,<NON_REF> 304.64 . ASSEMBLED_HAPS=41;BaseQRankSum=0.000;DP=18;ExcessHet=0.0000;FILTERED_HAPS=31;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=61200,18;ReadPosRankSum=-0.613 GT:AD:DP:GQ:PL:SB 0/1:8,8,0:16:99:312,0,312,336,336,672:4,4,2,6
6632+
chr9 81171416 . C T,<NON_REF> 304.64 . ASSEMBLED_HAPS=41;BaseQRankSum=0.000;DP=18;ExcessHet=0.0000;FILTERED_HAPS=21;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=61200,18;ReadPosRankSum=-0.613 GT:AD:DP:GQ:PL:SB 0/1:8,8,0:16:99:312,0,312,336,336,672:4,4,2,6
66346633
chr9 81171417 . T <NON_REF> . . END=81171417 GT:DP:GQ:MIN_DP:PL 0/0:18:54:18:0,54,806
66356634
chr9 81171418 . G <NON_REF> . . END=81171424 GT:DP:GQ:MIN_DP:PL 0/0:19:57:19:0,57,830
66366635
chr9 81171425 . T <NON_REF> . . END=81171460 GT:DP:GQ:MIN_DP:PL 0/0:22:60:20:0,60,862

‎src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/testGvcfBeforeRebaseUsingFlowModeAdvanced.expected.flowbased.vcf.idx‎

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