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.
more info on --forceValidOutput in GATK v3.5
according to the release notes, GATK v3.5 has a new engine-level option "--forceValidOutput" to enforce v4.2 of the VCF specifications.
How does this option work? For instance, does it replace missing genotypes in the GT field from "." to "./."? (This is required by Beagle v >= 4.0.)
I don't see information about this option on the "CommandLineGATK" page.