[FEATURE] Add target intervals to HaplotypeCaller & BQSR

[FriederikeHanssen]

GATK states here that capture target files should be supplied when running Base Recalibration:

By definition, exome sequencing and other targeted sequencing data don’t cover the entire genome, so most analyses can be
restricted to just the capture targets (genes or exons) to save processing time and enable scatter gather parallelism. In 
addition, there are some processing steps, such as BQSR, that should be restricted to the capture targets in order to 
eliminate off-target sequencing data, which is uninformative and is a source of noise.

https://gatk.broadinstitute.org/hc/en-us/articles/360035889551-When-should-I-restrict-my-analysis-to-specific-intervals-

Same for HaplotypeCaller:

https://gatk.broadinstitute.org/hc/en-us/community/posts/4403947098395-What-intervals-to-use-in-HaplotypeCaller-GenotypeGVCF-for-exome-data-sequenced-with-different-capture-kits

So far we are not doing this as far as I see.