Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

Some questions on QD

Hello GATK team,

I want to apply this to some GATK processed data I obtained from a reliable source. I noticed that the QD values (in my data) do not match the procedure explained here. Some questions for you:

1) For multi-sample VCFs, how is the QD value computed by GATK when more than one sample is non hom-ref? For instance in my case I will have different QDs as QD=QUAL/AD, for different values of AD. If I compute my own QDs and I want to apply these filters, will it be reliable to do such filtering using my own ODs?

2) Is there a chance of getting a value different from QD=QUAL/AD if a specific argument is specified when executing the variant calling function (i.e HaplotypeCaller)?

Thank you,

Carlos

Tagged:

Best Answer

Answers

  • cdenizcdeniz Member

    Hi @bhanuGandham,

    Yeah, I noticed the AD mistake. However, I've been calculating my QDs using QUAL/DP (as DP is the sum of the ADs). What I didn't know for sure was if DP = AD exclusively for non hom-ref ADs, therefore I assumed your initial equation might have been correct.

    Thank you, for the details upon the multi-sample QD.

    Carlos

Sign In or Register to comment.