Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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 for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Genomics Basics

As a general question, if you are aware of any reference or book for “Genomics for dummies” that explains a bit more about the algorithms used in the GATK pipeline that would be appreciated. I have already watched a lot of videos from the youtube channel: "Variant analysis with GATK course (2017)" but still cannot understand how each algorithm works. Thanks very much!


  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @ZLak,

    The Methods and Algorithms articles of the GATK website offers some insight into how the algorithms work. You might change the version setting to access the older documents as the internal algorithms haven't changed for existing tools.

  • ZLakZLak Member

    Hi @shlee,

    Thanks for your response. That is a great collection of information. Are you aware of any references that talks about Sort and MarkDuplicate stages in simple terms? I have already gone through This Article but I am going to need a more basic explanation of how both pipeline stages work. Also, knowing that both those steps are going to be IO-heavy, are you aware of any investigations on how to combine/merge the two steps into one?


  • SheilaSheila Broad InstituteMember, Broadie admin


    Unfortunately, we don't have anything more basic. Perhaps googling for some genomics books or terms will help. There are some great videos on youtube that talk about sequencing.


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