We used GATK version 4-beta4 TargetCoverageSexGenotyper module to infer sample's gender based on WGS data. However, we can't find this module in GATK 4.0.2 now. How can we infer gender information by the new version GATK?
The CNV workflows are in beta and are still evolving. I think the new tool you can use is DetermineGermlineContigPloidy.