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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.
Once you have identified variant sites in your data and assigned genotypes for each sample at those sites, it can be useful to further refine the genotypes, e.g. by phasing, by imputation, and by identifying Mendelian violations. The GATK includes tools for phasing and identifying Mendelian violations, but does not include imputation tools. However, we do provide conversion tools to interface with BEAGLE, a popular imputation tool developed at Washington University.
Geraldine Van der Auwera, PhD