I want to conduct a rare variant association test and incorporate site mutability as a covariate.

In the ExAC paper they show that site mutability between CpG sites, transitions and transversions are very different. As sites with higher background mutability are more likely to be noise I want to control for this.

Is there any tools available to annotate a set of variants depending on which above category they fall into?

I have chromosome, position, transcript consequence and protein consequence fields in my dataset.

Many thanks for any replies I receive