Add flanking sequence

In some situations, it is useful to see a variant in the context of the bases of the reference sequence. This information can be added using the Annotate with Flanking Sequence tool:

        Toolbox | Add Information to Variants (Image add_information_closed_16_n_p) | Add Flanking Sequence (Image gg_flanking_sequence)

This opens a dialog where you can select a variant track (Image variant_track_16_n_p) to be annotated.

Clicking Next will display the dialog shown in figure 22.3

Image annotate_flanking_step2
Figure 22.3: Specifying a reference sequence and the amount of flanking bases to include.

Select a sequence track that should be used for adding the flanking sequence, and specify how large the flanking region should be.

The result will be a new track with an additional column for the flanking sequence formatted like this: CGGCT[T]AGTCC with the base in square brackets being the variant allele.