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 about VQSR variant set if the reference not the hg38
There is a question when I run GATK. My goal is get variant from multiple sample in the rice. And I get a raw variant from HaplotypeCaller, and followed CombineGVCFs, GenotypeGVCFs according to the Best Practices. All looks good, but when I attempt to filter Variants, I chose the VQSR method which is recommend by you. (Because my sample number is enough to builds a model ). The question is when I run VariantRecalibrator, I need to input some variant set which is representative of true sites. I have no idea where to download those snp set, I need your help.
By the way, My reference is rice genome.