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.
reason for using -new-qual in GenotypeGVCFs
I am aware that -new-qual switch in GenotypeGVCFs uses a new algorithm to calculate AFs. Can I get more details of it with examples on why should it be used instead of the old one (about which also I would like to know)? On quick look, I saw that the variant quality (QUAL) was different for a particular variant site with and without the usage of -new-qual.