BreakTracer: Tracing inserted sequence fragments at structural variant breakpoints

BreakTracer is designed to identify inserted sequence fragments at structural variant (SV) breakpoints using long-read sequencing data. It can detect mobile element insertions, viral sequence integrations, and internal tandem duplications (ITDs), such as FLT3-ITDs. In contrast to generic SV callers like delly, BreakTracer can resolve complex SVs mediated by such insertions and link the inserted sequences to adjacent genomic rearrangements.