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.

Any recommended changes to Best Practices for genotyping-by-sequencing data?

mcrossleymcrossley Madison, WIMember

Hi, I saw a similar question to mine was posted a few years ago but didn't see an answer there.
I am specifically wondering about the pre-processing recommendations - like how duplicate mapping would affect genotyping-by-sequencing data.
Would it be okay for me to skip ahead to variant calling?
Thanks for any insight you can give,


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