Structural variant detection across sequencing technologies.

HitSV, a structural variant caller combining repetitiveness- and signature-density-aware breakpoint recognition with haplotype-resolved local assembly, delivers base-resolution SV reconstruction and genotyping across sequencing technologies. On HG002 it raised genotype F1 scores over state-of-the-art callers by 15-72% (long read), 10-36% (short read) and 12% (hybrid). It expanded the 1KGP phase 4 SV callset by 31.5% and identified tandem-repeat-mobile-element composite arrays as a prevalent complex SV class in a Chinese long-read cohort.