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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
This method is described to be the "First pass of the base quality score recalibration". What is the second pass? It is not mentioned anywhere, or am I looking in the wrong place? In v1.2 there were two steps, is there only one step now for bqsr?