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 to includeing loci of non-variant in GenotypeGVCFs step with GATK4?
I called germline short variants using haplotype caller with GATK 4.0, and then I want to extracted the non-variants and variants ** into seperate files so I could filter them seperately. In the GATK 3.x pipeline, there used to be **-allSites or --includeNonVariantSites in GenotypeGVCFs . Is it there no more in this new version?
Thanks in advance~