We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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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.
BQSR and -L
I'm working with whole genome data (in a non-model with no databases of known sites), and I'm wondered if using -L to speed things up by running each chromosome in parallel creates a problem? Specifically, by reducing the amount of data the recalibration is based off?