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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.
PCR Duplicate detection on PCR-Free Libraries
We've just started a big project in which we plan to use GATK with PCR-Free Libraries & I was curious as to what your thoughts are on using PCR Duplicate detection (MarkDuplicates) with the currently Illumina PCR-Free libraries? Internally do you still run this stage of the GATK pipeline with the new libraries?
Looking at your best practices documents I see it's still in there, but didn't see anything mentioning PCR-Free libraries.