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.
LOH detection using GATK4's somatic CNV workflow
Can GATK4's somatic CNV workflow detect copy-neutral LOH events for 1) tumor-only samples with a panel of normal (PON) or 2) tumor-normal pairs with a PON? I see that ModelSegments can give a "0" call, but it seems like that is for all high-quality neutral calls.