Overview of structural variant (SV) discovery and genotyping strategies using short-read, (Delly, Manta-Batch, Manta-Joint, Smoove), and long-read (CuteSV, Sniffles) based tools for kākāpō. Delly and Smoove each have their own in-built genotyping programs, while Manta, CuteSV and Sniffles do not. Variants called by Manta, CuteSV and Sniffles were genotyped using short-read data as input for the BayesTyper genotyping software package. Data were analysed in two steps: 1) An initial filtering threshold(s) for call quality step used for comparisons of SV type, size distributions and overlaps (in gold); and 2) genotype quality threshold(s) used to explore variability in number of SVs carried by individuals and genotype consistency among tools (in green). The proportion of SVs passing Mendelian Inheritance were estimated across a range of thresholds (Table 3).