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.

Simple explanation of MarkDuplicate

I am having a hard time understanding how MarkDuplicate works. Based on MarkDuplicate documentation, this is how it has been described: “The MarkDuplicates tool works by comparing sequences in the 5 prime positions of both reads and read-pairs in a SAM/BAM file.” I don’t understand what “5 prime positions” means in the above statement. Also, what does it mean in the context of “of both reads and read-pairs” ? If you could please explain that to me using an example I would really appreciate that.

Answers

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