This is an example from pichuan@ to run vg giraffe, so we can go from FASTQs --> BAM.
To test this, I got a machine using the command listed here: https://github.com/google/deepvariant/blob/r1.5/docs/deepvariant-details.md#command-for-a-cpu-only-machine-on-google-cloud-platform. I added more disks because 300G is not enough for the example below. I used --boot-disk-size "1000" for now.
(Note: the disk issue might be because I didn't run with --rm in docker.)