We call a variation large-scale when the changes do not fit into the sequence portion of a short read.
Paired-end read sequencing is then the methodology that allows us to identify where the reorganization took place. Pairs in the unexpected orientation, template sizes of unexpected lengths together can provide the necessary guidance to identify the "reorganization" junction points relative to the reference genome.
This recipe provides code that:
Creates a modified genome based on the reference.
Simulates sequencing reads from this modified genome
Aligns the simulated reads against the reference
Allow you to visualize the results in IGV
A detailed presentation that explains the steps and rationale for this recipe can be found at: