PacBio is selling ~10x PacBio SEQUEL long reads as an upgrade to Illumina data for SV discovery.
In a clinical setting, the main requirements are proper sensitivity and specificity but also the processing of cohorts, at least families. This requires a genotyping step, such that it can be identified whether a given variant is shared by two or more individuals or whether it is not.
What are the tools of the trade for this task?
As having 50-60x PacBio reads is not an option from a economic point of view, one has to make do with 10x coverage.