Annotate with 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 | Resequencing Analysis (Image resequencing) | Variant Annotation (Image variant_annotate_folder_closed_16_h_p) | Annotate with 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 27.32

Image annotate_flanking_step2
Figure 27.32: 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.