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.