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 27.70.

Image splicesiterefiner
Figure 27.70: 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.