Identify variants with effect on splicing

This tool will analyze a variant track to determine whether the variants fall within potential splice sites. First select your variant track (figure 26.3) followed by a transcript track (see figure 26.4). 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 26.3: Variant track selection.

Image predict_splice_site_effect2
Figure 26.4: 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 26.5).

Image predict_splice_site_effect3
Figure 26.5: Results of the predict splice site effect tool.