The Structural Variation algorithm

The Indels and Structural Variants detection 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.

The two steps of the structural variation algorithm is described in detail in Creating Left- and Right breakpoint signatures and Predicting Structural Variants.