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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.

UnifiedGenotyper - pooled data - multiple samples - ploidy of one pooled sample or all?

Thank you for developing a great set of tools and adding in the ploidy option to the UnifiedGenotyper! My question is in regards to the ploidy argument when calling multiple pooled samples together. If I have pooled samples from the same population at different time points and want to call SNPs with multiple sample awareness, do I use the ploidy of one sample or that of all samples. For example, if I have pooled samples of approximately 25 haploid genomes each from three different time points from the same population should I use 25 or 75 as my ploidy?

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