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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.
How to interpret Gaussian mixture model plots
I ran VQSR with 150+ whole genome samples. Attached is one of the Gaussian mixture model plots. I have read the VQSR guide on how to interpret the plots but I am not quite understand. Referring to the plot, green area represents good quality variants while variants fall in red area should be filtered out, the annotations MQ and QD are plotted against each other. For MQ, i can see that good quality variants have MQ around 60. What about QD? What can I do with these plots?