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.
Reference genome and VCF file
I am trying to analyse a non - human multi chromosome genome. I have also selected a vcf file to use a a source of known variant sites. Does the reference genome need the chromosomes to be in the same order as the VCF file? Or does it need to be alphanumerical?
Also, I think I need to modify the headers on the reference file so to match the names used on the vcf for the same chromosomes. Can you lease confirm this? Sorry for the noob questions.