The InDels and Structural Variants detection algorithm

The Indels and Structural Variants detection algorithm has two steps:

  1. Identify 'breakpoint signatures': First, the algorithm 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.
  2. Identify 'structural variant signatures': Secondly, the algorithm creates structural variant signatures from the identified breakpoint signatures. This is done by mapping the consensus unaligned ends of the identified LB and RB signatures to selected areas of the references as well as to each other. The mapping patterns of the consensus unaligned ends are examined and structural variant annotations consistent with the mapping patterns are created.