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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.
Limits on the size of a PoN
Due to a shortcoming in the Java interface of the underlying storage space (HDF5), a single matrix cannot exceed a number of bytes equal to MAX_INT, which is 2147483647
Therefore, S x T x 8 < 2147483647, where S is the number of samples and T is the number of targets.
In a simpler form: S x T < 268435455
This is usually only an issue for WGS PoNs. In this case, we recommend setting larger binsize (e.g. 5000) to avoid a very large number of targets (T).