Google Cloud - VCF Creation Support from .bam

Question

[DavidStreid]

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?

[GenoMax]

Take a look at this online documentation for ideas. Google genomics cookbook documentation.

[chiachun.chiu]

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: https://github.com/googlegenomics/pipelines-api-examples/tree/master/cwl_runner