Identify variants with effect on splicing

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 26.3.

Image effect_on_splicing_step1
Figure 26.3: Select the variant track that you wish to check for potential influence on splicing.

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 box you can choose to exclude all variants that do not fall within a splice site.