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.
How to combine gVCFs form different chromosomes
I have gVCFS genberated by haplotypecaller (gatk 3.5). 3 sets, 2 of them have same chromosome different samples, 200 each, and one has different chromosomes different samples. What would be the best way to GenotypeGVCFs in my case, would it accept these 3 sets of data.