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Check out the documentation at VariantAnnotator.
In https://www.broadinstitute.org/gatk/guide/article?id=1174, the link in "Check out the documentation at VariantAnnotator." (https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html) is broken.