The representation method of break point pos

[user-tq]

I used delly and sansa to build a structural variation analysis pipeline and attempted to evaluate its accuracy through NCCL validation data. Delly detected the expected mutation. But I'm a bit surprised why there is a 1 bp difference in the representation of breakpoints. answer: the sansa result:

[1]ANNOID	query.chr	query.start	query.chr2	query.end	query.id	query.qual	query.svtype	query.ct	query.svlen	query.startfeature	query.endfeature
None	7	55266405	7	92462404	INV00002766	7260	INV	3to3	37195999	EGFR(0;+)	CDK6(0;-)
None	22	23632600	9	133729450	BND00012515	10000	BND	5to3	0	BCR(0;+)	ABL1(0;+)

in delly.bcf

22	23632600	BND00012515	A	]9:133729450]A	10000	PASS	PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv1.1.6;END=23632601;CHR2=9;POS2=133729450;PE=431;MAPQ=60;CT=5to3;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=56;SRQ=1;CONSENSUS=AGAATAAAACTAATTTTTTCTCCCAATTTTCTCTTCCTTTTTCTTTTTTCTGTTCCCCCCTTTCTCTTCCAGAGTAAGTACTGGTTTGGGGAGGAGGGTTGCAGCGGCCGAGCCAGGGTCTCCACCCAGGAAGGACTCATCGGGCAGGGTGTGGGGAA;CE=1.97658;RDRATIO=1;SOMATIC	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	0/1:-253.075,0,-455.964:10000:PASS:222980:329282:106302:2:748:431:155:95    0/0:0,-75.2007,-857.843:10000:PASS:221127:323350:102223:2:1302:0:250:0
7	55266405	INV00002766	C	<INV>	7260	PASS	PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv1.1.6;END=92462404;PE=101;MAPQ=60;CT=3to3;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=60;INSLEN=0;HOMLEN=1;SR=20;SRQ=1;CONSENSUS=TAATGATGACTAAAGCAAGGGATTGTGATTGTTCATTCATGATCCCACTGCCTTCTTTTCTTGCTTCATCCTCGTGAGCCAGGGAGCTGCGCCCTCGCCATCTGGGGCCTCGCGCGCG;CE=1.97084;RDRATIO=0.997411;SOMATIC	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	0/1:-193.272,0,-528.756:10000:PASS:197626:345940:220737:2:577:101:173:77	0/0:0,-75.2167,-873.159:10000:PASS:197576:346736:220664:2:768:0:250:0

example the INV00002766，On the IGV image, it can be seen that soft splicing occurs on chromosome 7

between 55266405 and 55266406；

between 92462404 and 92462405

Perhaps it should be said that this is just a small descriptive questions of delly?I am quite concerned about whether there is a conversion between 1base and 0base?I understand that when annotating snv/indel, there is a requirement to annotate according to the 3 'rule of the transcript,Is there a similar requirement in structural variation?

This BND00012515 is particularly confusing for me, as the breakpoint seems to be "chr22 between 23632659-23632661" and "chr9 between 133729450-133729452",Why choose the current breakpoint?