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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.
When calculating Quality score, "Only “good bases” are included: those satisfying minimum base quality, mapping read quality, pair mapping quality and NQS". Can you please explain what you mean by NQS? And what is the different between Pair mapping quality and mapping read quality?