If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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

prasundutta87prasundutta87 EdinburghMember

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.


Best Answer


Sign In or Register to comment.