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.
VQSR for single sample exome/targeted regions
I read on the best practices slides that I should not use VQSR if the cohort is small. I only one sample for a single individual. I was wondering how useful it is to perform VQSR on this sample by using the GVCFs from 1000G? Am I losing a lot by not doing VQSR step for a single sample? I have some parameters in mind that I want the final VCF to satisfy: Min Q and Min depth.