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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Project level VCF

I am combining gVCFs that are processed exactly the same, I observed that most variants have this tag: "GT:AD:DP:GQ:PL". However for some variants, within the same variant, they can have this tag GT:AD:DP:GQ:PGT:PID:PL" for some of the samples but not others.

I did some testing
a) perform combineGVCF on a set of gVCF then do genotypeGVCF (test a)
b) perform genotypeGVCF only on this set of gVCF (test b)

What I observed is that there are some variants present only in test a, but not in test b. Same thing happens vice versa, i.e. variants present only in test b, but not in test a. These kind of variants all all got the same tag GT:AD:DP:GQ:PGT:PID:PL. Why is this the case? And what is combineGVCF and genotypeGVCF actually doing?


  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin
    We'll address the question about additional variants in the output in your other discussion thread.

    The tag differences you observe are due to some variants getting additional annotations that can be added when there are multiple variants within an active region. They are related to physical phasing. For more on this, please read the HaplotypeCaller documentation.
  • yyeeyyee Member

    Thanks for your comments.

    1) How would the phasing information affect the way the variants are being combined across different samples?

    2) how should we handle phasing information when generating project level VCF?

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin


    I don't think the phasing affects the way variants are combined across the samples. Can you please post some example records from the GVCFs and from testing a and b like you mentioned above. Specifically, I need to see the GVCF record from HaplotypeCaller and how the record differs after CombineGVCFs and GenotypeGVCFs.


Sign In or Register to comment.