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 25.69) followed by a transcript track (see figure 25.70). As part of the dialog you can choose to exclude all variants that do not fall within a splice site.
Figure 25.69: Variant track selection.
Figure 25.70: 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 25.71).
Figure 25.71: Results of the predict splice site effect tool.