[User Story] Update to GATK 4

[pbiology]

Need

As a hospital administrator I want the pipeline to use GATK version 4 rather than 3 as the license for GATK 4 is free to use, but GATK version 3 is not.

Suggested approach

Update all affected container to use GATK 4. If this is not deemed possible, we need to acquire a license for GATK 3

Considered alternatives

Alternative would be to not use GATK at all

Deviation

No response

System requirements assessed

• [ ] Yes, I have reviewed the system requirements

Requirements affected by this story

Won't affect any requirements as this is just a software update

Risk assessment needed

• [ ] Needed
• [ ] Not needed

Risk assessment

No response

SOUPs

No response

Can be closed when

We are no longer running GATK 3

Blockers

No response

Anything else?

Somewhat linked to #1375