[nvnieuwk]

This PR adds a new caller: gatk Mutect2. This expands the current selection of somatic variant callers.

Two new parameters were added:
--panel_of_normals and --panel_of_normals_tbi which are optional parameters used to specify a panel of normals for mutect2

[matthdsm]

Would it make sense to start differentiating between somatic/germline subwf here?

[nvnieuwk]

Would it make sense to start differentiating between somatic/germline subwf here?

I'm actually not sure we would really need differentiate this. Especially at this point since it's just a draft PR. I'm more thinking about doing something similar you did to the preprocessing pipeline and make all options sample-specific so users can configure the pipeline in whatever way they want

[matthdsm]

[nvnieuwk]

Currently VCF2DB does not work because bcftools norm does not correctly normalize FORMAT fields. I'll look into this later