Structural Variant (SV) types and common problems associated with short-read sequence data: A) deletion, called when reads do not map to, and/or are split across, a given region on the reference genome. Generally the most straightforward SV to detect with short-read data, but complex rearrangements may preclude mapping and result in a false call; B) duplication, typically identified by an increase in read depth, however reference error may result in a false call, preclude assessments of copy number variation, or miss sequence variation due to unmapped reads; C) insertion, short-reads may be mapped if the majority of each read aligns to the reference genome, but reads composed mostly of the insertion sequence may remain unmapped; D) inversion, breakpoints (i.e., exact positions of double-stranded DNA breaks) are difficult to resolve as they typically occur in highly repetitive regions; E) translocation, breakpoints difficult to resolve as they commonly occur in highly repetitive regions, reads may also incorrectly map to the ‘original’ chromosome from which the translocation arose. Further, it is common for more than one SV or different SV types to occur in close proximity. Resolving these complex SVs is particularly challenging with short-read sequence data as multiple mapping signals may contradict one another (e.g., multiple deletions in close proximity, deletions that overlap with inversion/translocation breakpoints), unless large samples sizes are used (Collins et al., 2020).