It looks like you're new here. If you want to get involved, click one of these buttons!
This article is part of the Best Practices workflow documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow.
Whether your callset is big or small, you'll probably need to evaluate it against others, or query it to identify the variants that are relevant to your work. The GATK offers multiple ways to perform these tasks efficiently at scale. For this step, we do not provide a standardized workflow because it depends too much on the needs of individual projects. However, our documentation provides a number of concrete examples of what you can do with these tools.
Geraldine Van der Auwera, PhD