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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.
scatter-gather for BaseRecalibrator
I'm trying to figure out whether BaseRecalibrator requires a custom gather function in GATK 3.1-1? Can I just sent the .scatterCount property and will GATK gather things appropriately? Or do I need to use a custom gatherer? If so, has anyone developed on? I see online for BQSR but I'm not sure if that's the same thing as BaseRecalbrator.
Thanks (from a newbie)