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 29.24) followed by a transcript track (see figure 29.25). As part of the dialog you can choose to exclude all variants that do not fall within a splice site.

Image predict_splice_site_effect1
Figure 29.24: Variant track selection.

Image predict_splice_site_effect2
Figure 29.25: 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 29.26).

Image predict_splice_site_effect3
Figure 29.26: Results of the Predict Splice Site Effect tool.