1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
|
##fileformat=VCFv4.2
##reference=file:///Homo_sapiens.GRCh37.GATK.illumina.fasta
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Placeholder field to accomodate VCF parsing tools that require a GT field.">
##ALT=<ID=INS,Description="Insertion">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of the SV">
##INFO=<ID=SUPP_SEQ,Number=.,Type=String,Description="Supporting sequencing technologies">
##INFO=<ID=SUPP_VAL,Number=.,Type=String,Description="Supporting validation technologies">
##INFO=<ID=GENE,Number=.,Type=String,Description="Gene(s) overlap in breakpoint">
##INFO=<ID=CLUSTER,Number=.,Type=String,Description="IDs of other clustered breakpoints">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT COLO829T
1 87337011 truthset_1_1 T T]10:36119127] . PASS MATEID=truthset_1_2;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_41 GT 0/1
1 118516186 truthset_2_1 T T[1:118516222[ . PASS MATEID=truthset_2_2;SVLEN=36;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=SPAG17;CLUSTER=. GT 0/1
1 118516222 truthset_2_2 T ]1:118516186]T . PASS MATEID=truthset_2_1;SVLEN=36;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=SPAG17;CLUSTER=. GT 0/1
1 207981231 truthset_3_1 G G[1:208014822[ . PASS MATEID=truthset_3_2;SVLEN=33591;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,10X;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=. GT 0/1
1 208014822 truthset_3_2 G ]1:207981231]G . PASS MATEID=truthset_3_1;SVLEN=33591;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,10X;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=. GT 0/1
1 224646603 truthset_4_1 A ]1:224800120]A . PASS MATEID=truthset_4_2;SVLEN=153517;SVTYPE=DUP;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=truthset_5 GT 0/1
1 224782795 truthset_5_1 C C[1:224786034[ . PASS MATEID=truthset_5_2;SVLEN=3239;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=BIONANO;GENE=.;CLUSTER=truthset_4 GT 0/1
1 224786034 truthset_5_2 C ]1:224782795]C . PASS MATEID=truthset_5_1;SVLEN=3239;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=BIONANO;GENE=.;CLUSTER=truthset_4 GT 0/1
1 224800120 truthset_4_2 A A[1:224646603[ . PASS MATEID=truthset_4_1;SVLEN=153517;SVTYPE=DUP;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=truthset_5 GT 0/1
3 24565108 truthset_6_1 T [3:24566182[T . PASS MATEID=truthset_6_2;SVLEN=1074;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_7,truthset_8,_truthset_9,truthset_10,truthset_18,truthset_43 GT 0/1
3 24566182 truthset_6_2 T [3:24565108[T . PASS MATEID=truthset_6_1;SVLEN=1074;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_7,truthset_8,_truthset_9,truthset_10,truthset_18,truthset_43 GT 0/1
3 25400602 truthset_7_1 G G[12:72666892[ . PASS MATEID=truthset_7_2;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=CAPTURE;GENE=TRHDE;CLUSTER=truthset_6,truthset_8,truthset_9,truthset_10,truthset_18,truthset_43 GT 0/1
3 25401059 truthset_8_1 G G[10:60477224[ . PASS MATEID=truthset_8_2;SVTYPE=BND;SUPP_SEQ=ILL,ONT;SUPP_VAL=CAPTURE;GENE=BICC1;CLUSTER=truthset_6,truthset_7,truthset_9,truthset_10,truthset_18,truthset_43 GT 0/1
3 26431918 truthset_9_1 T [6:26194041[T . PASS MATEID=truthset_9_2;SVTYPE=BND;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR;GENE=.;CLUSTER=truthset_6,truthset_7,truthset_8,truthset_10,truthset_18,truthset_43 GT 0/1
3 26663922 truthset_10_1 G G]3:26664499] . PASS MATEID=truthset_10_2;SVLEN=577;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=CAPTURE;GENE=LRRC3B;CLUSTER=truthset_6,truthset_7,truthset_8,truthset_9,truthset_18,truthset_43 GT 0/1
3 26664499 truthset_10_2 G G]3:26663922] . PASS MATEID=truthset_10_1;SVLEN=577;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=CAPTURE;GENE=LRRC3B;CLUSTER=truthset_6,truthset_7,truthset_8,truthset_9,truthset_18,truthset_43 GT 0/1
3 60132754 truthset_11_1 T T[3:60204543[ . PASS MATEID=truthset_11_2;SVLEN=71789;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,BIONANO;GENE=FHIT;CLUSTER=. GT 0/1
3 60204543 truthset_11_2 T ]3:60132754]T . PASS MATEID=truthset_11_1;SVLEN=71789;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,BIONANO;GENE=FHIT;CLUSTER=. GT 0/1
3 60872124 truthset_12_1 C C[3:61013215[ . PASS MATEID=truthset_12_2;SVLEN=141091;SVTYPE=DEL;SUPP_SEQ=ILL,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=FHIT;CLUSTER=. GT 0/1
3 61013215 truthset_12_2 C ]3:60872124]C . PASS MATEID=truthset_12_1;SVLEN=141091;SVTYPE=DEL;SUPP_SEQ=ILL,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=FHIT;CLUSTER=. GT 0/1
3 186442175 truthset_13_1 T T[3:186513634[ . PASS MATEID=truthset_13_2;SVLEN=71459;SVTYPE=DEL;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=KNG1,RFC4;CLUSTER=. GT 0/1
3 186513634 truthset_13_2 T ]3:186442175]T . PASS MATEID=truthset_13_1;SVLEN=71459;SVTYPE=DEL;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=KNG1,RFC4;CLUSTER=. GT 0/1
4 66211957 truthset_14_1 T ]4:66212037]T . PASS MATEID=truthset_14_2;SVLEN=80;SVTYPE=DUP;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=EPHA5;CLUSTER=. GT 0/1
4 66212037 truthset_14_2 T T[4:66211957[ . PASS MATEID=truthset_14_1;SVLEN=80;SVTYPE=DUP;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=EPHA5;CLUSTER=. GT 0/1
4 187996322 truthset_15_1 T ]4:187996382]T . PASS MATEID=truthset_15_2;SVLEN=60;SVTYPE=DUP;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=CAPTURE;GENE=.;CLUSTER=. GT 0/1
4 187996382 truthset_15_2 T T[4:187996322[ . PASS MATEID=truthset_15_1;SVLEN=60;SVTYPE=DUP;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=CAPTURE;GENE=.;CLUSTER=. GT 0/1
5 28787996 truthset_16_1 T T[5:28963096[ . PASS MATEID=truthset_16_2;SVLEN=175100;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
5 28963096 truthset_16_2 T ]5:28787996]T . PASS MATEID=truthset_16_1;SVLEN=175100;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
5 178973288 truthset_17_1 C C[5:178973321[ . PASS MATEID=truthset_17_2;SVLEN=33;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=CAPTURE;GENE=.;CLUSTER=. GT 1/1
5 178973321 truthset_17_2 C ]5:178973288]C . PASS MATEID=truthset_17_1;SVLEN=33;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=CAPTURE;GENE=.;CLUSTER=. GT 1/1
6 26194041 truthset_9_2 T [3:26431918[T . PASS MATEID=truthset_9_1;SVTYPE=BND;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR;GENE=.;CLUSTER=truthset_6,truthset_7,truthset_8,truthset_10,truthset_18,truthset_43 GT 0/1
6 26194117 truthset_18_1 G G]6:26194406] . PASS MATEID=truthset_18_2;SVLEN=289;SVTYPE=INV;SUPP_SEQ=ILL;SUPP_VAL=CAPTURE;GENE=.;CLUSTER=truthset_6,truthset_7,truthset_8,truthset_9,truthset_10,truthset_43 GT 0/1
6 26194406 truthset_18_2 G G]6:26194117] . PASS MATEID=truthset_18_1;SVLEN=289;SVTYPE=INV;SUPP_SEQ=ILL;SUPP_VAL=CAPTURE;GENE=.;CLUSTER=truthset_6,truthset_7,truthset_8,truthset_9,truthset_10,truthset_43 GT 0/1
6 138774059 truthset_19_1 T [15:23717166[T . PASS MATEID=truthset_19_2;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=NSHL1;CLUSTER=truthset_20,truthset_52,truthset_53,truthset_54 GT 0/1
6 138774181 truthset_20_1 G G]15:23712617] . PASS MATEID=truthset_20_2;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=NSHL1;CLUSTER=truthset_19,truthset_52,truthset_53,truthset_54 GT 0/1
7 52440354 truthset_21_1 T T[7:52440387[ . PASS MATEID=truthset_21_2;SVLEN=33;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=. GT 0/1
7 52440387 truthset_21_2 T ]7:52440354]T . PASS MATEID=truthset_21_1;SVLEN=33;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=. GT 0/1
7 57471577 truthset_22_1 C C[7:57496111[ . PASS MATEID=truthset_22_2;SVLEN=24534;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
7 57496111 truthset_22_2 C ]7:57471577]C . PASS MATEID=truthset_22_1;SVLEN=24534;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
7 77981839 truthset_23_1 C C[7:78082248[ . PASS MATEID=truthset_23_2;SVLEN=100409;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=MAGI2;CLUSTER=. GT 0/1
7 78082248 truthset_23_2 C ]7:77981839]C . PASS MATEID=truthset_23_1;SVLEN=100409;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=MAGI2;CLUSTER=. GT 0/1
7 78190206 truthset_24_1 G G[7:78257685[ . PASS MATEID=truthset_24_2;SVLEN=67479;SVTYPE=DEL;SUPP_SEQ=ILL,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=MAGI2;CLUSTER=. GT 0/1
7 78257685 truthset_24_2 G ]7:78190206]G . PASS MATEID=truthset_24_1;SVLEN=67479;SVTYPE=DEL;SUPP_SEQ=ILL,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=MAGI2;CLUSTER=. GT 0/1
7 85844668 truthset_25_1 A ]7:85853700]A . PASS MATEID=truthset_25_2;SVLEN=9032;SVTYPE=DUP;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
7 85853700 truthset_25_2 A A[7:85844668[ . PASS MATEID=truthset_25_1;SVLEN=9032;SVTYPE=DUP;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
7 104485068 truthset_26_1 T ]7:104612302]T . PASS MATEID=truthset_26_2;SVLEN=127234;SVTYPE=DUP;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=LHFPL3;CLUSTER=. GT 0/1
7 104612302 truthset_26_2 T T[7:104485068[ . PASS MATEID=truthset_26_1;SVLEN=127234;SVTYPE=DUP;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=LHFPL3;CLUSTER=. GT 0/1
7 110393332 truthset_27_1 T T[7:110394461[ . PASS MATEID=truthset_27_2;SVLEN=1129;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=IMMP2L;CLUSTER=. GT 0/1
7 110394461 truthset_27_2 T ]7:110393332]T . PASS MATEID=truthset_27_1;SVLEN=1129;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=IMMP2L;CLUSTER=. GT 0/1
7 125746125 truthset_28_1 G G[7:126166901[ . PASS MATEID=truthset_28_2;SVLEN=420776;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=GRM8;CLUSTER=. GT 0/1
7 126098490 truthset_29_1 G [7:126167441[G . PASS MATEID=truthset_29_2;SVLEN=68951;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=GRM8;CLUSTER=. GT 0/1
7 126166901 truthset_28_2 G ]7:125746125]G . PASS MATEID=truthset_28_1;SVLEN=420776;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=GRM8;CLUSTER=. GT 0/1
7 126167441 truthset_29_2 G [7:126098490[G . PASS MATEID=truthset_29_1;SVLEN=68951;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=GRM8;CLUSTER=. GT 0/1
7 143959226 truthset_30_1 G G[7:144088794[ . PASS MATEID=truthset_30_2;SVLEN=129568;SVTYPE=DEL;SUPP_SEQ=ILL,PB;SUPP_VAL=PCR;GENE=ARHGEF34P;CLUSTER=. GT 0/1
7 144088794 truthset_30_2 G ]7:143959226]G . PASS MATEID=truthset_30_1;SVLEN=129568;SVTYPE=DEL;SUPP_SEQ=ILL,PB;SUPP_VAL=PCR;GENE=ARHGEF34P;CLUSTER=. GT 0/1
7 150746657 truthset_31_1 C C[15:84810725[ . PASS MATEID=truthset_31_2;SVTYPE=BND;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=ASIC3;CLUSTER=. GT 0/1
8 112062420 truthset_32_1 T T[8:112063583[ . PASS MATEID=truthset_32_2;SVLEN=1163;SVTYPE=DEL;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=. GT 0/1
8 112063583 truthset_32_2 T ]8:112062420]T . PASS MATEID=truthset_32_1;SVLEN=1163;SVTYPE=DEL;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=. GT 0/1
8 131248116 truthset_33_1 T ]8:131274647]T . PASS MATEID=truthset_33_2;SVLEN=26531;SVTYPE=DUP;SUPP_SEQ=ILL;SUPP_VAL=PCR,BIONANO;GENE=ASAP1;CLUSTER=. GT 0/1
8 131274647 truthset_33_2 T T[8:131248116[ . PASS MATEID=truthset_33_1;SVLEN=26531;SVTYPE=DUP;SUPP_SEQ=ILL;SUPP_VAL=PCR,BIONANO;GENE=ASAP1;CLUSTER=. GT 0/1
9 28031835 truthset_34_1 A A]9:28059140] . PASS MATEID=truthset_34_2;SVLEN=27305;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=LINGO2;CLUSTER=truthset_35,truthset_36 GT 0/1
9 28031863 truthset_35_1 C [9:28034467[C . PASS MATEID=truthset_35_2;SVLEN=2604;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=LINGO2;CLUSTER=truthset_34,truthset_36 GT 0/1
9 28034299 truthset_36_1 C C[9:28157692[ . PASS MATEID=truthset_36_2;SVLEN=123393;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=LINGO2;CLUSTER=truthset_34,truthset_35 GT 0/1
9 28034467 truthset_35_2 C [9:28031863[C . PASS MATEID=truthset_35_1;SVLEN=2604;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=LINGO2;CLUSTER=truthset_34,truthset_36 GT 0/1
9 28059140 truthset_34_2 A A]9:28031835] . PASS MATEID=truthset_34_1;SVLEN=27305;SVTYPE=INV;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=LINGO2;CLUSTER=truthset_35,truthset_36 GT 0/1
9 28157692 truthset_36_2 C ]9:28034299]C . PASS MATEID=truthset_36_1;SVLEN=123393;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=LINGO2;CLUSTER=truthset_34,truthset_35 GT 0/1
9 114293052 truthset_37_1 T T[9:114293097[ . PASS MATEID=truthset_37_2;SVLEN=45;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=NOT_VALIDATED;GENE=ZNF483;CLUSTER=. GT 0/1
9 114293097 truthset_37_2 T ]9:114293052]T . PASS MATEID=truthset_37_1;SVLEN=45;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=NOT_VALIDATED;GENE=ZNF483;CLUSTER=. GT 0/1
10 7059512 truthset_38_1 T ]19:17396810]T . PASS MATEID=truthset_38_2;SVTYPE=BND;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=ANKLE1;CLUSTER=truthset_39,truthset_40 GT 0/1
10 7132874 truthset_39_1 A A[19:17397644[ . PASS MATEID=truthset_39_2;SVTYPE=BND;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=ANKLE1;CLUSTER=truthset_38,truthset_40 GT 0/1
10 7634373 truthset_40_1 A [18:9868617[A . PASS MATEID=truthset_40_2;SVTYPE=BND;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=ITIH5;CLUSTER=truthset_38,truthset_39 GT 0/1
10 33386453 truthset_41_1 T T[10:36119061[ . PASS MATEID=truthset_41_2;SVLEN=2732608;SVTYPE=DEL;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_1 GT 0/1
10 36119061 truthset_41_2 T ]10:33386453]T . PASS MATEID=truthset_41_1;SVLEN=2732608;SVTYPE=DEL;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_1 GT 0/1
10 36119127 truthset_1_2 T T]1:87337011] . PASS MATEID=truthset_1_1;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_41 GT 0/1
10 55476347 truthset_42_1 C C[10:55476896[ . PASS MATEID=truthset_42_2;SVLEN=549;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=CAPTURE;GENE=.;CLUSTER=. GT 0/1
10 55476896 truthset_42_2 C ]10:55476347]C . PASS MATEID=truthset_42_1;SVLEN=549;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=CAPTURE;GENE=.;CLUSTER=. GT 0/1
10 60477224 truthset_8_2 G ]3:25401059]G . PASS MATEID=truthset_8_1;SVTYPE=BND;SUPP_SEQ=ILL,ONT;SUPP_VAL=CAPTURE;GENE=BICC1;CLUSTER=truthset_6,truthset_7,truthset_9,truthset_10,truthset_18,truthset_43 GT 0/1
10 60477422 truthset_43_1 G G]12:72667075] . PASS MATEID=truthset_43_2;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=CAPTURE;GENE=BICC1,TRHDE;CLUSTER=truthset_6,truthset_7,truthset_8,truthset_9,truthset_10,truthset_18 GT 0/1
10 83641806 truthset_44_1 T T[10:83827666[ . PASS MATEID=truthset_44_2;SVLEN=185860;SVTYPE=DEL;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=NRG3;CLUSTER=. GT 0/1
10 83827666 truthset_44_2 T ]10:83641806]T . PASS MATEID=truthset_44_1;SVLEN=185860;SVTYPE=DEL;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=NRG3;CLUSTER=. GT 0/1
10 89700299 truthset_45_1 A A[10:89712341[ . PASS MATEID=truthset_45_2;SVLEN=12042;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=PTEN;CLUSTER=. GT 1/1
10 89712341 truthset_45_2 A ]10:89700299]A . PASS MATEID=truthset_45_1;SVLEN=12042;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=PTEN;CLUSTER=. GT 1/1
11 80785600 truthset_46_1 T T[11:81093780[ . PASS MATEID=truthset_46_2;SVLEN=308180;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
11 81093780 truthset_46_2 T ]11:80785600]T . PASS MATEID=truthset_46_1;SVLEN=308180;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
12 72666892 truthset_7_2 G ]3:25400602]G . PASS MATEID=truthset_7_1;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=CAPTURE;GENE=TRHDE;CLUSTER=truthset_6,truthset_8,truthset_9,truthset_10,truthset_18,truthset_43 GT 0/1
12 72667075 truthset_43_2 G G]10:60477422] . PASS MATEID=truthset_43_1;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=CAPTURE;GENE=BICC1,TRHDE;CLUSTER=truthset_6,truthset_7,truthset_8,truthset_9,truthset_10,truthset_18 GT 0/1
12 92161147 truthset_47_1 C C[12:92161182[ . PASS MATEID=truthset_47_2;SVLEN=35;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=. GT 0/1
12 92161182 truthset_47_2 C ]12:92161147]C . PASS MATEID=truthset_47_1;SVLEN=35;SVTYPE=DEL;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=. GT 0/1
12 129771777 truthset_48_1 N <INS> . PASS SVLEN=255;SVTYPE=INS;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR;GENE=TMEM132D;CLUSTER=. GT 0/1
14 73014649 truthset_49_1 T T[14:73014746[ . PASS MATEID=truthset_49_2;SVLEN=96;SVTYPE=INS;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=RGS6;CLUSTER=. GT 0/1
14 73014746 truthset_49_2 T ]14:73014649]T . PASS MATEID=truthset_49_1;SVLEN=96;SVTYPE=INS;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=RGS6;CLUSTER=. GT 0/1
14 104560088 truthset_50_1 G G[14:104560143[ . PASS MATEID=truthset_50_2;SVLEN=55;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=NOT_VALIDATED;GENE=ASPG;CLUSTER=. GT 1/1
14 104560143 truthset_50_2 G ]14:104560088]G . PASS MATEID=truthset_50_1;SVLEN=55;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=NOT_VALIDATED;GENE=ASPG;CLUSTER=. GT 1/1
14 106333876 truthset_51_1 A <INS> . PASS SVLEN=100;SVTYPE=INS;SUPP_SEQ=ONT,PB;SUPP_VAL=PCR;GENE=.;CLUSTER=. GT 0/1
15 23685608 truthset_52_1 C [20:37274468[C . PASS MATEID=truthset_52_2;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_19,truthset_20,truthset_53,truthset_54 GT 0/1
15 23706879 truthset_53_1 C ]20:37274667]C . PASS MATEID=truthset_53_2;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_19,truthset_20,truthset_52,truthset_54 GT 0/1
15 23712617 truthset_20_2 G G]6:138774181] . PASS MATEID=truthset_20_1;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=NSHL1;CLUSTER=truthset_19,truthset_52,truthset_53,truthset_54 GT 0/1
15 23717166 truthset_19_2 T [6:138774059[T . PASS MATEID=truthset_19_1;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=NSHL1;CLUSTER=truthset_20,truthset_52,truthset_53,truthset_54 GT 0/1
15 23831660 truthset_54_1 A A]15:23992700] . PASS MATEID=truthset_54_2;SVLEN=161040;SVTYPE=INV;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_19,truthset_20,truthset_52,truthset_53 GT 0/1
15 23992700 truthset_54_2 A A]15:23831660] . PASS MATEID=truthset_54_1;SVLEN=161040;SVTYPE=INV;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_19,truthset_20,truthset_52,truthset_53 GT 0/1
15 41621294 truthset_55_1 A ]15:41628506]A . PASS MATEID=truthset_55_2;SVLEN=7212;SVTYPE=DUP;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=OIP5,NUSAP1;CLUSTER=. GT 0/1
15 41628506 truthset_55_2 A A[15:41621294[ . PASS MATEID=truthset_55_1;SVLEN=7212;SVTYPE=DUP;SUPP_SEQ=ILL,ONT;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=OIP5,NUSAP1;CLUSTER=. GT 0/1
15 84810725 truthset_31_2 C ]7:150746657]C . PASS MATEID=truthset_31_1;SVTYPE=BND;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=ASIC3;CLUSTER=. GT 0/1
16 58624545 truthset_56_1 T T[16:58663331[ . PASS MATEID=truthset_56_2;SVLEN=38786;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=CNOT1;CLUSTER=. GT 1/1
16 58663331 truthset_56_2 T ]16:58624545]T . PASS MATEID=truthset_56_1;SVLEN=38786;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=CNOT1;CLUSTER=. GT 1/1
16 78928636 truthset_57_1 G G[16:79095007[ . PASS MATEID=truthset_57_2;SVLEN=166371;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=WWOX;CLUSTER=. GT 0/1
16 79095007 truthset_57_2 G ]16:78928636]G . PASS MATEID=truthset_57_1;SVLEN=166371;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=WWOX;CLUSTER=. GT 0/1
18 9868617 truthset_40_2 A [10:7634373[A . PASS MATEID=truthset_40_1;SVTYPE=BND;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=ITIH5;CLUSTER=truthset_38,truthset_39 GT 0/1
18 66379461 truthset_58_1 C C[18:66382826[ . PASS MATEID=truthset_58_2;SVLEN=3365;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=TMX3,CCDC102B;CLUSTER=. GT 0/1
18 66382826 truthset_58_2 C ]18:66379461]C . PASS MATEID=truthset_58_1;SVLEN=3365;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=TMX3,CCDC102B;CLUSTER=. GT 0/1
19 17396810 truthset_38_2 T T[10:7059512[ . PASS MATEID=truthset_38_1;SVTYPE=BND;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=ANKLE1;CLUSTER=truthset_39,truthset_40 GT 0/1
19 17397644 truthset_39_2 A ]10:7132874]A . PASS MATEID=truthset_39_1;SVTYPE=BND;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=ANKLE1;CLUSTER=truthset_38,truthset_40 GT 0/1
20 13160729 truthset_59_1 C C[20:13164103[ . PASS MATEID=truthset_59_2;SVLEN=3374;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
20 13164103 truthset_59_2 C ]20:13160729]C . PASS MATEID=truthset_59_1;SVLEN=3374;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 0/1
20 14962957 truthset_60_1 G G[20:15013948[ . PASS MATEID=truthset_60_2;SVLEN=50991;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=MACROD2;CLUSTER=truthset_61 GT 0/1
20 15000623 truthset_61_1 A A[20:15013842[ . PASS MATEID=truthset_61_2;SVLEN=13219;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=MACROD2;CLUSTER=truthset_60 GT 0/1
20 15013842 truthset_61_2 A ]20:15000623]A . PASS MATEID=truthset_61_1;SVLEN=13219;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB;SUPP_VAL=PCR,CAPTURE;GENE=MACROD2;CLUSTER=truthset_60 GT 0/1
20 15013948 truthset_60_2 G ]20:14962957]G . PASS MATEID=truthset_60_1;SVLEN=50991;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=MACROD2;CLUSTER=truthset_61 GT 0/1
20 33219526 truthset_62_1 C C[20:33219569[ . PASS MATEID=truthset_62_2;SVLEN=49;SVTYPE=DEL;SUPP_SEQ=ONT,PB;SUPP_VAL=PCR;GENE=PIGU;CLUSTER=. GT 0/1
20 33219569 truthset_62_2 C ]20:33219526]C . PASS MATEID=truthset_62_1;SVLEN=49;SVTYPE=DEL;SUPP_SEQ=ONT,PB;SUPP_VAL=PCR;GENE=PIGU;CLUSTER=. GT 0/1
20 37274468 truthset_52_2 C [15:23685608[C . PASS MATEID=truthset_52_1;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_19,truthset_20,truthset_53,truthset_54 GT 0/1
20 37274667 truthset_53_2 C C[15:23706879[ . PASS MATEID=truthset_53_1;SVTYPE=BND;SUPP_SEQ=ILL;SUPP_VAL=PCR,CAPTURE;GENE=.;CLUSTER=truthset_19,truthset_20,truthset_52,truthset_54 GT 0/1
22 33759249 truthset_63_1 A A[22:33838399[ . PASS MATEID=truthset_63_2;SVLEN=79150;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=LARGE;CLUSTER=. GT 0/1
22 33838399 truthset_63_2 A ]22:33759249]A . PASS MATEID=truthset_63_1;SVLEN=79150;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=LARGE;CLUSTER=. GT 0/1
X 31196943 truthset_64_1 A A[X:31216211[ . PASS MATEID=truthset_64_2;SVLEN=19268;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=DMD;CLUSTER=. GT 0/1
X 31216211 truthset_64_2 A ]X:31196943]A . PASS MATEID=truthset_64_1;SVLEN=19268;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=DMD;CLUSTER=. GT 0/1
X 31301203 truthset_65_1 T T[X:32038750[ . PASS MATEID=truthset_65_2;SVLEN=737547;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=DMD;CLUSTER=. GT 0/1
X 32038750 truthset_65_2 T ]X:31301203]T . PASS MATEID=truthset_65_1;SVLEN=737547;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE;GENE=DMD;CLUSTER=. GT 0/1
X 32077855 truthset_66_1 G G[X:32293097[ . PASS MATEID=truthset_66_2;SVLEN=215242;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=DMD;CLUSTER=. GT 0/1
X 32098532 truthset_67_1 A A[X:32201251[ . PASS MATEID=truthset_67_2;SVLEN=102719;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=DMD;CLUSTER=. GT 0/1
X 32201251 truthset_67_2 A ]X:32098532]A . PASS MATEID=truthset_67_1;SVLEN=102719;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=DMD;CLUSTER=. GT 0/1
X 32293097 truthset_66_2 G ]X:32077855]G . PASS MATEID=truthset_66_1;SVLEN=215242;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=DMD;CLUSTER=. GT 0/1
X 34059778 truthset_68_1 C C[X:34062705[ . PASS MATEID=truthset_68_2;SVLEN=2927;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 1/1
X 34062705 truthset_68_2 C ]X:34059778]C . PASS MATEID=truthset_68_1;SVLEN=2927;SVTYPE=DEL;SUPP_SEQ=ILL,ONT,PB,10X;SUPP_VAL=PCR,CAPTURE,BIONANO;GENE=.;CLUSTER=. GT 1/1
|
