Multi-pass local realignment
As described in Method
the algorithm initially builds the realignment graph using the input read mapping. After the graph has been built the algorithm realigns individual reads based on information inferred from the realignment graph structure and its associated metadata. In some cases repetitive realignment iterations yield even more improvements, because with each realignment iteration the structure of the realignment graph changes slightly, potentially permitting further improvements. Local realignment therefore supports to perform multiple iterations implicitly. This is not only considered a convenience feature, but also saves a great deal of runtime by avoiding repeated transfers of large input data sets. For most samples local realignment will quickly saturate in the number of improvements. Generally, two realignment passes are strongly recommended. More than three passes rarely yield further improvements.