BND records in VCF can't be mated

[maxineliu]

Research organism: bufo; Scaffolds of reference genome: 11 chromosomes and more than 700 unplaced contigs; Each sample bam file is split into three parts because sniffles run with error when taking the whole bam file as input; There is no "CHR2" info in the VCF. My BND records are like:

NC_058080.1	2	Sniffles2.BND.57M0	N	[NW_025334187.1:745476[N	56	PASS	PRECISE;SVTYPE=BND;SUPPORT=3;COVERAGE=None,0,8,8,8;STRAND=+-;AC=5;STDEV_LEN=0.000;STDEV_POS=1.095;SUPP_VEC=011010110100	GT:GQ:DR:DV:ID	./.:0:0:0:NULL	0/1:17:8:4:Sniffles2.BND.1133DFS0	0/1:7:1:1:Sniffles2.BND.F91DDS0	./.:0:0:0:NULL	1/1:5:0:2:Sniffles2.BND.119BB5S0	./.:0:0:0:NULL	0/0:2:8:2:Sniffles2.BND.10C58DS0	0/1:37:8:6:Sniffles2.BND.10E918S0	./.:0:0:0:NULL	0/0:15:9:1:Sniffles2.BND.111C8AS0	./.:0:0:0:NULL	./.:0:0:0:NULL
NC_058080.1	22930	Sniffles2.BND.58M0	N	N[NC_058081.1:438603307[	52	PASS	PRECISE;SVTYPE=BND;SUPPORT=4;COVERAGE=12,1,9,7,7;STRAND=+-;AC=1;STDEV_LEN=0;STDEV_POS=0;SUPP_VEC=000000000100	GT:GQ:DR:DV:ID	0/0:0:8:0:NULL	0/0:0:25:0:NULL	0/0:0:17:0:NULL	0/0:0:10:0:NULL	0/0:0:31:0:NULL	0/0:0:13:0:NULL	0/0:0:20:0:NULL	0/0:0:10:0:NULL	0/0:0:7:0:NULL	0/1:8:2:4:Sniffles2.BND.111C90S0	0/0:0:10:0:NULL	0/0:0:11:0:NULL
NC_058080.1	44289	Sniffles2.BND.59M0	N	N[NC_058082.1:616349849[	60	PASS	PRECISE;SVTYPE=BND;SUPPORT=2;COVERAGE=48,39,39,12,12;STRAND=+-;AC=1;STDEV_LEN=0.000;STDEV_POS=1.000;SUPP_VEC=010000101010	GT:GQ:DR:DV:ID	0/0:0:40:0:NULL	0/0:60:35:1:Sniffles2.BND.1133ECS0	0/0:0:50:0:NULL	0/0:0:39:0:NULL	0/0:0:58:0:NULL	0/0:0:38:0:NULL	0/0:60:38:1:Sniffles2.BND.10C59CS0	0/0:0:49:0:NULL	0/1:6:12:4:Sniffles2.BND.CB9A2S0	0/0:0:47:0:NULL	0/0:55:27:2:Sniffles2.BND.100A8AS0	0/0:0:54:0:NULL

And I can't find the mated BND records even manually. For example, Sniffles2.BND.58M0's mated breakend should locate at NC_058081.1:438603307. But the BND records close to NC_058081.1:438603307 are like:

NC_058081.1	438581495	Sniffles2.BND.465E0M1	N	[NC_058082.1:397550826[N	45	PASS	PRECISE;SVTYPE=BND;SUPPORT=4;COVERAGE=19,4,18,19,3;STRAND=+-;AC=1;STDEV_LEN=0;STDEV_POS=0;SUPP_VEC=000010000000	GT:GQ:DR:DV:ID	0/0:0:8:0:NULL	./.:0:2:0:NULL	0/0:0:8:0:NULL	0/0:0:9:0:NULL	0/1:12:10:4:Sniffles2.BND.11A7B4S1	./.:0:1:0:NULL	./.:0:2:0:NULL	0/0:0:9:0:NULL	./.:0:2:0:NULL	./.:0:4:0:NULL	0/0:0:12:0:NULL	0/0:0:17:0:NULL
NC_058081.1	438600037	Sniffles2.BND.4660EM1	N	N]NC_058082.1:510224996]	56	PASS	PRECISE;SVTYPE=BND;SUPPORT=2;COVERAGE=11,4,17,15,15;STRAND=+-;AC=1;STDEV_LEN=0.000;STDEV_POS=6.269;SUPP_VEC=010000111100	GT:GQ:DR:DV:ID	0/0:0:17:0:NULL	0/0:5:9:2:Sniffles2.BND.114091S1	0/0:0:21:0:NULL	0/0:0:14:0:NULL	0/0:0:30:0:NULL	./.:0:2:0:NULL	0/1:9:11:4:Sniffles2.BND.10E39AS1	0/0:19:14:2:Sniffles2.BND.113761S1	0/0:9:7:1:Sniffles2.BND.CE09FS1	0/0:20:11:1:Sniffles2.BND.10E01FS1	0/0:0:10:0:NULL	0/0:0:29:0:NULL
NC_058081.1	438723627	Sniffles2.BND.4663BM1	N	N]NC_058083.1:108873495]	59	PASS	PRECISE;SVTYPE=BND;SUPPORT=3;COVERAGE=10,1,12,12,17;STRAND=-;AC=1;STDEV_LEN=0;STDEV_POS=0;SUPP_VEC=000010000000	GT:GQ:DR:DV:ID	0/0:0:7:0:NULL	./.:0:4:0:NULL	0/0:0:8:0:NULL	0/0:0:8:0:NULL	0/1:16:5:3:Sniffles2.BND.11A7CDS1	./.:0:2:0:NULL	0/0:0:7:0:NULL	0/0:0:11:0:NULL	./.:0:4:0:NULL	0/0:0:5:0:NULL	./.:0:4:0:NULL	./.:0:4:0:NULL

Is it normal? If not, what factors result in this situation (such as splitting bam)?

Thanks, Maxine