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.


when using scatter with CombineGVCFs walkers I get the following error: "You have asked for an interval that cuts in the middle of one or more gVCF blocks. Please note that this will cause you to lose records that don't end within your interval"
CombineGVCFs need to see all the data at once? Or at least all the chromosome at once? If it need it, I think the automatic scatter-gather for this class in scala script is working by 'LOCI' instead of 'CONTIG'.


Best Answer


  • ecuencaecuenca Member

    I have not included the intervals file (-L) and padding (-ip) for CombineGVCFs now and the error I posted previously has disappeared.
    Intervals file were already applied to the Haplotype Caller so I'm thinking I don't need to use them again when combining, right?
    Also the speed is hugely improved: without scattering, for a 200 samples CombineGVCFs was expected to take about 17days (all exome) and it's only 30 hours if you don't include the intervals file and padding.
    Scattering (40) does in about 6 minutes what was done in about 1h.

  • ecuencaecuenca Member

    Hi Geraldine,
    I was not sure if I was going to get a reply posting it at the forum, that's why I posted it again as a question to the GATK team. Sorry about that, never again, ;)

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    Thanks Ester. We try to reply to every single posting, regardless of where it is; it just sometimes takes an extra day if we're very busy (which we are right now...). If you're ever worried that your posting has been forgotten, you can just comment again in the same thread to ping us (but please do this sparingly).

Sign In or Register to comment.