use filtered variants in tmb and signatures

[ericblanc20]

Is your feature request related to a problem? Please describe.
In case of noisy data, the tumor mutational burden and the mutational signatures should be computed after filtration, rather than before.

Describe the solution you'd like
The steps and the corresponding wrappers should be able to adapt to somatic variant annotations and/or filtration.

Describe alternatives you've considered
None, really...