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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,


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