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.
Picard SortVcf changing VCF file version
I am using Picard SortVcf to reorder the order to match the order of my reference genome and BAM files. And it works great, however it seems to be changing the VCF format from 4.0 to 4.2, and this is incompatible with the downstream steps I need it for. Is there any workaround for this?