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.
Can Picard LiftoverVcf handle Indels?
Dear GATK team,
I have successfully run Picard LiftoverVcf on SNPs only data but when Combined with Indels, the results file is empty.
I use Picard version: 2.18.16. I now wonder if Picard LiftoverVcf is able to handle SNPs. If not, which tool would you recommend? For instance, would LiftOverIntervalList work for Indels?