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.

scatter-gather for BaseRecalibrator

estif74estif74 Saint Paul, MN, USAMember

Hi there,

I'm trying to figure out whether BaseRecalibrator requires a custom gather function in GATK 3.1-1? Can I just sent the .scatterCount property and will GATK gather things appropriately? Or do I need to use a custom gatherer? If so, has anyone developed on? I see online for BQSR but I'm not sure if that's the same thing as BaseRecalbrator.

Thanks (from a newbie)


  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    Hi Steve,

    No need to develop your own gatherer, there is already one in Queue (the BQSR Gatherer that you probably found).

    BQSR is short for Base Quality Score Recalibration, which we often use interchangeably with BaseRecalibrator, even though that's not technically correct (BQSR is the procedure, BaseRecalibrator is the main tool involved). Sorry for the confusion.

  • estif74estif74 Saint Paul, MN, USAMember

    OK got it. That's great. Thank you (and the GATK team) for your hard work. Now to get this working on the cluster here rather than my MacBook pro!!!

Sign In or Register to comment.