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 November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

GATK Guide Book

Having the "Table of Contents" in the back of the GATK Guide Book, caused me considerable time and trouble. I spent hours scanning through pages, looking for topics, for several days, before I found the Table of Contents in the back. I would be surprised if I am the only one this has happened to. Could I respectfully request that you move it to the front?



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah, sorry to hear that. The full TOC is at the back due to a quirk of the pdf generation library I used (because it's dynamically created). I don't have the time to mcguyver a solution to put it up front, but I could add an overview TOC that points to the fully detailed TOC, if that would help.

  • Nick_BeesonNick_Beeson Member

    Please do that. If on page 2 below the current content you place a red box with something like
    Table of Contents found on page 330
    it would be a great boon to other newbs.
    Adobe is idiotic for doing it this way. Every technical book I have read, and I have read many, has the ToC in the front.
    I almost did not post this complaint since I knew there was a good (bad?) reason, and did not want to rag on you.
    Thanks for your kind response.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    No worries, as long as the criticism is constructive it's always appreciated.

    This is not Adobe's fault though -- I used a free php-to-pdf library, and it's not quite pro-level publishing software. Was primarily supposed to be a free and fast way to dump a static versioned copy of the online content, but I'm delighted to hear people are actually using it as guide book as well. Sorry if it's a bit wonky. Will make more improvements over time -- but there never seems to be enough time.

  • Nick_BeesonNick_Beeson Member

    No there is never enough time. I recognize that in the entire set of GATK (manuals, this forum, and programs). You are under tight budgets as are we all, have heavy works loads, and want to maximize your output. All of which leads to understandable omissions or oddities. I am in complete sympathy with your efforts and appreciate your manual enormously.

    Now that I have the ToC I just noticed that it is "off by one", e.g. it says the "Data Processing Pipeline" section starts on page 63, but it actually starts on page 59 which the ToC lists as the start point for "Creating Variant Validation Sets". Oh well I can cope with that.

    You have answered my question, Thanks.

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