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.
Possible bug in BeagleOutputToVCF
It appears that BeagleOutputToVCF does not produce the expected result for the very first variant. Looking a little into it, I found out that the problem stems form the beagle.r2 file not having a header and the first line been treated as such instead of being read as a variant. Adding a bogus header line in the beagle.r2 file seems to be a fine workaround.