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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.
Possible bug in BeagleOutputToVCF
It appears that BeagleOutputToVCF does not produce the expected result for the very first variant. Looking a little into it, I found out that the problem stems form the beagle.r2 file not having a header and the first line been treated as such instead of being read as a variant. Adding a bogus header line in the beagle.r2 file seems to be a fine workaround.