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.
SelectVariants with --removeUnusedAlternates option.
I am using SelectVariants with --removeUnusedAlternates option. The unused alleles get removed but the INFO anf FORMAT field data associated with the removed allele does not get removed. Is there an additional option I need to specify or is this a known issue?