Thanks for taking the time to read the blog and comment- these are great questions! There are a couple of interesting points to make here. One is that many of these tools for discovering complex SVs are still relatively new, and the research community is still trying to understand that best methods for identifying and comparing these events. However, sequencing a large cohort of individuals would be very useful for us to understand the extent of these events within the population. This sort of study would also help refine our bioinformatic tools and interpretation of these events. There as a study called the 1000 Genomes project that was instrumental in setting standards for identifying small variants and for helping us understand the extent of small variation in the population. I'd love to see a '1000 Haplotypes' project to allow us to do the same thing for haplotypes and complex variants. We need to sequence more normal genomes in order to help interpret patient genomes.
While there is still some research to do, I expect prices to come down and hopefully we'll be able to analyze more genomes (patients and non-patients) at haplotype resolution.