Sample BH15700_1 shows a complex duplication-triplication-duplication structure as highlighted in aCGH data with SegDups and LCRs highlighted (orange bars). Sniffles2 identifies the inversion breakpoint at Jct2 (teal bar) but cannot fully resolve the entire allele including Jct1 as it is also not possible to be reported in the VCF standard. Red arrows indicate duplicated regions, and blue arrows show triplicated portions. One possible haplotype structure for a DUP-TRP/INV-DUP is shown with the triplication and initial duplication being inverted, forming Jct1 and Jct2 (ref. 34 ).
