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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
Varian quality recalibration annotations.
What annotations are recommended to be used for the variant recalibrator for an exome sequencing project? I am using the Ion proton system so my VCF files are automatically generated after the sequencing run. Also, would I still have to mark duplicates and realign indels in my BAM files before viewing them on a genome viewer like IGV? Since I already have my VCF files, I don't know if this will be necessary.
Thank you, these forums are very helpful!