Results

The mean individual mapping depth of short-reads for chromosomes was ~18x, and ranged from ~9x to ~38x. Of the 10 individuals sequenced using long-reads, seven met the minimum depth threshold of 4x coverage for long-read SV discovery. The mean individual mapping depth of long-reads for chromosomes was ~10x, and ranged from ~4x to ~16x. There was considerable variability in the number of SVs initially detected by each of the six strategies (herein datasets), with the most being the Manta-Batch and fewest being the CuteSV dataset (Table 1). In addition, inversions were the most common SV type detected in short-read discovery tools, while deletions were more common in long-read SV discovery tools. This pattern was consistent across call quality and genotype filtering thresholds (Table 1). The proportion of SVs passing call quality thresholds also varied, with Delly retaining the lowest proportion of SVs (~4%). Both the Manta-Batch and -Joint call quality filters retained roughly 26% of variants, whereas 27% of CuteSV and 32% of Sniffles variants were retained. The Smoove call set retained the highest proportion of SVs with ~68% passing call quality thresholds (Table 1). It is notable that the size distribution of filtered SVs varied between each of the SV discovery tools and that all reported insertions in Delly were below the minimum size threshold of 50bp (Table 2).