What is the best way to use Google Cloud/Genomics to create VCF files from .bam files? Is there specialized support or a package, or should I create a VM and install tools like GATK to do this?
Take a look at this online documentation for ideas. Google genomics cookbook documentation.
Use Genomics Pipeline API or other workflow languages (CWL or WDL/Cromwell) supported by Genomics API to construct a pipeline, and then build/push docker images for each tool you need to container registry. Finally, launch the pipeline. Another way is to use Google Dataflow, but I'm not familiar with this method :(
You can read the documents and source codes of this example from Google Genomics Cookbook:
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