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Genomics in the Cloud: Using Docker, GATK, and WDL in Terra

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all,

just noticed a book "Genomics in the Cloud: Using Docker, GATK, and WDL in Terra" that is authored by Geraldine.
https://www.amazon.com/dp/1491975199/

may I ask -- when is the book going to be available ? thank you !

-- bogdan

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Bogdan, you found me out :)

    We're almost done with the writing; the book is going into production in early January so it should be coming out in March 2020 if all goes well. Two chapters went up for Early Release this week, in fact, so if you have a Safari subscription I believe you can already check it out here: https://learning.oreilly.com/library/view/genomics-in-the/9781491975183/

    I'll post on the GATK blog when we have a more definitive timeline. Here's the full book table of contents:

    01 - Introduction
    02 - Genomics in a nutshell: a primer for newcomers to the field
    03 - Computing technology basics for life scientists
    04 - First steps on the Cloud
    05 - First steps with GATK
    06 - Best Practices for germline short variant discovery
    07 - Best Practices for somatic variant discovery
    08 - Automating analysis execution with WDL workflows
    09 - Deciphering real genomics workflows
    10 - Running single workflows at scale with Pipelines API
    11 - Running many workflows conveniently in Terra
    12 - Interactive analysis with Jupyter Notebooks in Terra
    13 - Assembling your own workspace in Terra
    14 - Making a fully reproducible paper

    Chapter titles are not yet final so if you find any of them confusing, let me know!

  • BogdanBogdan Palo Alto, CAMember ✭✭

    Dear Geraldine, wonderful news !

    we wish you lots of inspiration and energy with the writing, and we are looking forward reading the book ! it is going to be a great resource for all of us ! thank you for doing it .. :)

    we wish you and your family happy holidays, a Merry Christmas, and a fruitful and successful 2020 !

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