If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.

What are the parameters used by GATK to define a SNP?

I'm a master student and I'm using GATK, for the first time, to find SNP in RNAseq data. I would like to know what GATK considers a SNP. What are the parameters used for this, such as: frequency and number of reads aligned at the position of SNP.



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