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.
Transform VCF file changing only variant ids
I want to read a VCF file and write out another VCF file that is equivalent to the first one except that variant ids have been changed. How would I do that? A VCFFileReader gives me an iterator of VariantContext - can I get a copy of a VariantContext with everything identical except for variant id?