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BroadE Workshop 2015 March 19-20: Best Practices for Variant Calling with the GATK

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin
edited August 2015 in Archive

The full GATK team presented this workshop at the Broad Institute with support form the BroadE education program.

This workshop covered the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. The presentation materials describe why each step is essential to the calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.

The workshop materials are available at this link if you're viewing this post in the forum, or below if you are viewing the presentation page already.

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Geraldine Van der Auwera, PhD

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Comments

  • qiangfuqiangfu BelgiumMember Posts: 7

    Hello,

    This workshop is really very interesting and this is the latest one as well. I really would like to check the videos for the presentation, as not all information is in the slides. However, the videos available at http://www.broadinstitute.org/partnerships/education/broade/best-practices-variant-calling-gatk-1 does not work anymore. Would it be possible to fix them or make them available on other sites, such as youtube?

    Many thanks.

    Qiang FU

  • SheilaSheila Broad InstituteMember, Broadie, Moderator, Dev Posts: 4,583 admin

    @qiangfu
    Hi Qiang FU,

    I just tried a few of the videos on the site, and they work for me. Can you try watching them again? Are there only a few specific videos that do not work?

    Thanks,
    Sheila

  • qiangfuqiangfu BelgiumMember Posts: 7

    hi, Sheila,

    Upon seeing your reply, I tried it again on another computer, indeed they are working. It seems the issue is with the machine and/or the browser that I use. Am I sorry that I did not think of this, as I had not encountered any issue with video in this browser and the messages I got from the player says that the resource are not reachable ...

    Thanks for your help.

    Best
    Qiang FU

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

    One of our new devs mentioned he had the same problem and realized it was because he didn't have flash player installed. We're going to talk to the folks at Broad who provide the video hosting to see if we can make things easier for everyone to access the videos.

    Geraldine Van der Auwera, PhD

  • tamu_anandtamu_anand indMember Posts: 3

    There seems to be some problems with playing videos - see attached screenshot

    BroadE_Error.PNG
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  • SheilaSheila Broad InstituteMember, Broadie, Moderator, Dev Posts: 4,583 admin

    @tamu_anand
    Hi,

    I just tried on my computer using Google Chrome, and that video works for me. What browser are you using?

    -Sheila

  • ramiro2kramiro2k Member Posts: 11

    Hello, we teach a bioinformatics class at the University of Vermont, can we use some of your slides?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin
    Yes that's fine, as noted in response to your other question (no need to ask the same question several times, we read and respond to all postings).

    Geraldine Van der Auwera, PhD

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