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 30.24) followed by a transcript track (see figure 30.25). A variants that falls within a certain distance of an intron-exon boundary will be annotated as a possible splice site disruption (see figure 30.26). The distance is determined by the parameter Splice site window size. In the filter group you can choose to exclude all variants that do not fall within a splice site.

Image predict_splice_site_effect1
Figure 30.24: Variant track selection.

Image predict_splice_site_effect2
Figure 30.25: Transcript track selection.

Image predict_splice_site_effect3
Figure 30.26: Results of the Predict Splice Site Effect tool.