We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
Variant discovery starting from gVCF file
Hello, as the title suggests I'm looking to use the variant discovery tools, specifically SNP discovery. However I am not starting with a FASTA or BAM file, indeed I do not currently have access to them, instead I'm starting with a gVCF file that many of the relevant commands such as haplotype caller do not accept gVCFs as input, and for those commands that do use gVCFs it is implied that they should have been produced by haplotype caller.