For this, you need to specify zone and region in Dataflow API (as well as the Pipelines API if you are using Docker). For example, in order to restrict job processing to Europe, update the zone and region as follows:
# Dataflow API.
COMMAND="/opt/gcp_variant_transforms/bin/vcf_to_bq ... \
--region europe-west1 \
--zone europe-west1-b"
# Pipelines API.
gcloud alpha genomics pipelines run ... \
--zones europe-west1-b
If running from GitHub, you just need to specify zone and region for Dataflow API as below.
python -m gcp_variant_transforms.vcf_to_bq ... \
--region europe-west1 \
--zone europe-west1-b
You can choose the region for the BigQuery dataset at dataset creation time.