The current GATK version is 3.7-0
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1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

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Then follow instructions in Article#1894.

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Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

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Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

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?

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Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    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.

  • 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

    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.

  • 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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