The Structural Variation Plug-in algorithm has two steps. First, it identifies positions in the mapping(s) with an excess
of reads with left (or right) unaligned ends. For each of these, it creates a Left breakpoint (LB) or Right breakpoint (RB) signature. Second, it maps the consensus unaligned ends of the identified LB and RB signatures to selected areas of the references. The mapping patterns of the consensus unaligned ends are examined and structural variant annotations consistent with the mapping patterns are created.
Below we describe the two steps of the algorithm in detail.