This may not be the most helpful answer, but mutational burden can be calculated any of these ways. It's difficult to compare apples-to-apples among studies unless you say explicitly how you're doing it. You may be interested in the number of mutations per coding MB or per exon, which you'll be able to get from your annotation. If you have a large variability in coverage/depth among samples, you'll want to make sure that you take this into account so you don't bias the calculations due to false positives or false negatives.

This paper is a decent starting place outlining some of the different challenges and ways of estimating tumor mutational burden in a clinical setting.