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The full GATK team presented this workshop at the Broad Institute with support form the BroadE education program.
This workshop covered the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. The presentation materials describe why each step is essential to the calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.
The workshop materials are available at this link if you're viewing this post in the forum, or below if you are viewing the presentation page already.