GATK Mutect2 - investigate missing calls

[marchoeppner]

We find that some apparently obvious calls are not made when running Mutect2 (paired or single) - a reason is not immediately evident. The same positions are reliably called with Strelka. Possible reasons could involve a) parameterization (pipeline runs with mostly defaults) and b) alignment pre-processing (the pipeline is focused more on non-GATK tools and may not implement a perfect BAM post-processing workflow as required by GATK).