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BroadE Workshop 2013 Oct 21-22: GATK Best Practices & Queue

Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,712 admin
edited October 2014 in Presentations

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

This workshop included two modules:

  • Best Practices for Variant Calling with the GATK

    The core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. View the workshop materials to learn 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.

  • Building Analysis Pipelines with Queue

    An introduction to the Queue pipelining system. View the workshop materials to learn about how to use Queue to create analysis pipelines, scatter-gather them and run them locally or in parallel on a computing farm.

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Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

BP_workflow_large.png
1905 x 938 - 136K

Comments

  • michaelchaomichaelchao Member Posts: 16

    Dear GATK,

    I've been following the Best Practices workflow (using GenomeAnalysisTK-2.7-4-g6f46d11) on 50 human exome sequencing samples. After the VASQ stage, my vcf file contained around 7.5 million variants, but I'm only expecting around 200,000 variants. Could you please shed some light on what might be the cause?

    Thank you for your help.

  • michaelchaomichaelchao Member Posts: 16

    Dear GATK, this issue has been solved.

  • buddejbuddej St. LouisMember Posts: 28

    Is there any way the links to the PDFs could be fixed? Thanks!

    Issue · Github
    by Geraldine_VdAuwera

    Issue Number
    29
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,712 admin

    Sorry about that, will look into this right away.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,712 admin

    Fixed, thanks for reporting this @buddej

    Geraldine Van der Auwera, PhD

  • buddejbuddej St. LouisMember Posts: 28

    Thanks for the updates, @Geraldine_VdAuwera. Two of the Queue PDF links still don't work, but the gatk/events/slides/1310/ directory is browseable, so I was able to find the PDFs.

    The file names are just a little off ( GATKwh2-Q-1-Intro_to_Queue.pdf vs. GATKwh2-Q-1-Intro.pdf; GATKwh2-Q-4-Advanced_Queue.pdf vs. GATKwh2-Q-4-Advanced_Queue_capabilities.pdf )

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,712 admin

    Whoops, sorry about that too -- fixed now.

    Geraldine Van der Auwera, PhD

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