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.
gatk4 Allelic CNV
I have been using gatk4 alpha for copy number analysis. I have created PoN and did segmentation. Now I want to check for allelic CN which requires heterozygous sites. For now I am using germline heterozygous variants. is it okay ? Are there any suggestion on selecting variants ?