You can use Chutzpah for that
With Chutzpah you can run your tests from command line and integrate your tests with Visual Studio Test Explorer.
Chutzpah allows you decide if you want to run the tests from .ts files, .js files, .html files or from all of them.
When set (in Visual Studio/Tools/Options/Chutzpah) to run tests from .ts files, you will be able to analyze code coverage of your generated .js files, with a link between the generated JavaScript code and the .ts file that generated it.
It makes really easy to work on your TypeScript code coverage, even being the JavaScript code the real code under test.
You can install Chutzpah from Visual Studio/Tools/Extensions and updates.
You can find here more details about code coverage using Chutzpah.