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This article is part of the Best Practices workflow documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow.
It's all well and good to have a bunch of variant sites and genotypes, but how can you know whether they might be biologically relevant? That's where functional annotation comes in; this is the process of adding annotations to variant sites that tell you whether they fall within a coding or regulatory region, whether the mutation is sense or nonsense, etc. The GATK does not include any tool that perform functional annotation as such, but it does include conversion tools that allow you to interface with the popular annotation program SnpEff.
Geraldine Van der Auwera, PhD