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.
How many "-an" arguments in VariantRecalibrator should be used ?
I encountered a problem when using VariantRecalibrator function of GATK.
The following error often came out when I used the several common “-an” augments.
“##### ERROR MESSAGE: Bad input: Found annotations with zero variance. They must be excluded before proceeding.”
When I decreased the number of “-an”, another error came out.
ERROR MESSAGE: No data found.
I am confused about the “-an” argument. Which of them should be used?