Annotate with Effect Scores

The Annotate with Effect Scores tool annotates SNV variants with precomputed effect scores. An effect score indicates the impact of a mutation on the gene or transcript. Synonymous mutations have low impact, whereas mutations introducing premature stop-codons or altering protein structures have high impact. Typically, scores are given in a range from 0 to 1, where 1 indicates completely neutral mutations and 0 indicates deleterious mutations, the range and interpretation does however depend on the score used.

To run the Annotate with Effect Scores tool, go to:

        Toolbox | Resequencing Analysis (Image resequencing) | Variant Annotation (Image variant_annotate_folder_closed_16_h_p) | Annotate with Effect Scores (Image effect_scores_16_n_p)

Select the variant track (Image variant_track_16_n_p) as input, when you click Next you will need to provide four tracks with effect scores (see figure 22.2). The track Effect score A contains the precomputed effect scores of SNVs where the new allele is A. The other three tracks are defined similarly.

Image effect_score_selection
Figure 22.2: Select Effect Score tracks.

The tool outputs a variant track with an Effect score annotation added.