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 calling variants on pooled samples, is removing duplicates recommended?
I was planning to call variants on my pooled bacteria sample using GATK UnifiedGenotyper and was wondering if removing duplicates should be in the best practices since with pooled samples, the reads might not be PCR duplicates but actually reads from different strains that I have in the pool. I would appreciate any input from your side. Thank you