Difference in the size distributions of reported indels/CNVs in published personal genome sequencing studies. The graphs show variation found in a few personal genome sequencing studies [1–4, 6–8]. These diagrams indicate that multiple approaches are needed for better detection of CNVs. Here, the total variant set in the Venter genome found in both the Levy et al.  and the current study is displayed. Unlike the current study where the size of mate-pair indels is equal to the difference between the mapping distance and the expected insert size, the SVs in the Ahn et al.  study are only based on the mapping distance. Besides the NGS data, we have also included the variants detected by the high density Agilent 24 M data in the Kim et al.  study. In Wheeler et al. , insertions identified by intra-read alignment would be limited by the size of the sequencing read; hence, large insertions beyond the read length were not detected. Wang et al. , Kim et al., and McKernan et al.  detected small variants based on split-reads and large ones based on mate-pairs and microarrays, but failed to detect variation between these size ranges. Also, see Additional file 1. (a) Insertion and duplication size distribution. (b) Deletion size distribution.