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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.
HaplotypeCaller - ploidy for pooled samples of bacterial genomes
I have an experiment where I've sequenced pools of individuals from bacterial populations. Based on the guidelines for setting ploidy, I think I should set this to the average read depth because I don't know how many individuals are in each sample (but the number of individuals greatly exceeds the read depth). Does this make sense? If so, should I set the ploidy individually for each library (I have 96 in total), or is it okay to take the average depth across all libraries as an approximation and use the same value for all libraries.