Predict Splice Site Effect
This tool will analyze a variant track to determine whether the variants fall within potential splice sites. First select your variant track (figure 29.25) followed by a transcript track (see figure 29.26). As part of the dialog you can choose to exclude all variants that do not fall within a splice site.
Figure 29.25: Variant track selection.
Figure 29.26: Transcript track selection.
If a variant falls within two base pairs of an intron-exon boundary, it will be annotated as a possible splice site disruption (see figure 29.27).
Figure 29.27: Results of the Predict Splice Site Effect tool.