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.
UnifiedGenotyper: metrics for quality score (and pics)
I was wondering, in the vcf output from UnifiedGenotyper what metrics go into the variant quality score, QUAL ?
I'm assuming that depth, DP is one of them but I can't find further information. Apologies if I've missed it.
Attached are some plots of the depth and quality distribution for variant calls, and also of the relationship between depth and quality. I'm slightly worried that the bimodal quality distribution indicates an error, otherwise I've just attached the graphs for general interest.