Heads up:
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.

VariantFiltration and VariantRecalibrator


I have 2 questions:
I want to use the VariantFiltration after HaplotypeCaller. There are different filtering recommendations for SNPs and INDELs. How should I run the VariantFiltration? Should I create a separated vcf for SNPs and INDELs or is there a mode to use?

The second question is regarding VariantRecalibrator. It is recommended to run it with several samples. What does it mean - these samples should be family related or should they be from the same sequencing run? Since, currently I run each sample separately, but I do have many samples to analyze. All were sequenced at the same sequencing platform, by the same lab, but not necessarily at the same sequencing run. Can I use all together for the VariantRecalibrator?

Many thanks for your help,


Sign In or Register to comment.