How to run the Local Realignment tool

The tool is found in the Toolbox:

        Toolbox | NGS Core Tools (Image ngs_folder_open_16_n_p) | Local Realignment (Image alignment_16_n_p)

Select one or multiple read mappings as input. If one read mapping is selected, local realignment will attempt to realign all contained reads, if appropriate. If multiple read mappings are selected, their reference genome must exactly match. Local realignment will realign all reads from all input read mappings as if they came from the same input. However, local realignment will create one output read mapping for each input read mapping, thereby preserving the affiliation of each read to its sample. Clicking Next allows you to set parameters as displayed in figure 21.30.

Image local_realignment_step4
Figure 21.30: Set the realignment options.

Alignment settings

Guidance-variant settings

The next dialog allows specification of the result handling. Under "Output options" it is possible to specify whether the results should be presented as a reads track or a stand-alone read mapping (figure 21.31).

Image local_realignment_resulthandling
Figure 21.31: An output track of realigned regions can be created.

If enabled, the option Output track of realigned regions will cause the algorithm to output a track of regions that help pinpoint regions that have been improved by local realignment. This track has purely informative intention and cannot be used for anything else.