Predict splice site effect
This tool will analyze a variant track to determine whether the variants fall within potential splice sites. A transcript track has to be selected as shown in figure 27.64.
Figure 27.64: The splice site annotation.
If a variant falls within two base pairs of an intron-exon boundary, it will annotated as a possible splice site disruption. As part of the dialog you can choose to exclude all variants that do not fall within a splice site.