Uprade GATK to v4.3.0 for gCNV variant calling.

[holtgrewe]

Is your feature request related to a problem? Please describe.
At the moment, gCNV uses per-sample calls in case mode. Families are then joined with merge_cohort_vcfs which has issues because reference calls are not marked as such consistently.

Describe the solution you'd like
The gCNV docs that "It is possible to analyze multiple samples simultaneously in a case mode command. Provide each sample with -I.".

We should do this and thus perform the case mode analysis per family. However, it is unclear how much this will help as gCNV docs also say "PostprocessGermlineCNVCalls consolidates the scattered GermlineCNVCaller results, performs segmentation and calls copy number states. The tool generates per-interval and per-segment sample calls in VCF format and runs on a single sample at a time."

Describe alternatives you've considered
N/A

Additional context

• Github Issue says family calling can be improved: CNV VCFs could be improved broadinstitute/gatk#6167

[holtgrewe]

Note: since 4.2.0.0, gCNV has a pipeline for joint gCNV exome joint calling.