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?

sp580sp580 GermanyMember

Hello!

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 Ti/Tv of 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 1.803826 to 1.929386.

I do not see how 1.7 summarizes a range of numbers from 1.8 to 1.9. What am I missing?

Thanks in advance and happy new year!

Best Answer

Answers

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hello @sp580, This may due to the inclusion of the flanking regions in the summarized Ti/Tv calculation. Take a look at this explanation here. As an experiment, you could reduce your flanking region and see if that affects these metrics.

  • sp580sp580 GermanyMember
    edited January 6

    Thanks @AdelaideR
    I went through the document again, and cannot find a way to do what you are suggesting.

    Also looked again the details here and here.

    Could you please provide me with more specific information on how to understand the discrepancies between both Ti/Tv ratios?

    Thanks!

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @sp580 I want to make sure that I have the most correct answer for you, so I am asking someone on our team who works with the statistical analysis directly. I will get back to you once I find your answer.

Sign In or Register to comment.