Conservation scores can be computed by several tools e.g. PhyloP and PhastCons and can be downloaded as pre-computed scores from an whole genome alignment of different species from different sources. See how to find and import tracks with conservation scores in Import tracks.
Toolbox | Resequencing () | Functional Consequences | Annotate with Conservation Score
Select the variant track as input and when you click Next you will need to provide the track with conservation scores (see figure 26.42).
In the resulting track, all the variants will have quality scores annotated, and this can be used for sorting and filtering the track (see Showing a track in a table).