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.
VariantRecalibrator across multiple VCFs with identical positions but different annotations
I have a set of VCFs with identical positions in them:
1 10097 . T . 26 . AN=196;DP=1622;MQ=20.06;MQ0=456 GT:DP
1 10097 . T . 21.34 . AN=198;DP=2338;MQ=19.53;MQ0=633 GT:DP
1 10097 . T . 11.70 . AN=240;DP=3957;MQ=19.74;MQ0=1085 GT:DP
1 10097 . T . 15.56 . AN=134;DP=1348;MQ=18.22;MQ0=442 GT:DP
If I use all of them as input for VariantRecalibrator, which annotations will VariantRecalibrator use? Should I instead merge the VCFs with CombineVariants and run VariantAnnotator, before I run VariantRecalibrator?
I'm not sure if the forum is for asking technical questions only or you are allowed to ask for best practices as well. Feel free to delete my question, if it doesn't belong here. Thank you.