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 () | Variant Annotation () | Annotate with Effect Scores ()
Select the variant track () 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.
The tool outputs a variant track with an Effect score annotation added.