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 does Picard's CollectVariantCallingMetrics calculates novel Ti/Tv per sample and as summary?
I am having a hard time making sense of the novel Ti/Tv values produced by Picard's
CollectVariantCallingMetrics when comparing the summary and the detailed reports.
The summary reports a novel
1.700175 (which is the same value found in tranche 90 of the
VariantRecalibrator's tranches plot). However, sample-wise, novel
Ti/Tv ranges from
I do not see how
1.7 summarizes a range of numbers from
1.9. What am I missing?
Thanks in advance and happy new year!