Best Practices for Variant Discovery in DNAseq

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,192Administrator, GATK Developer admin

This article is part of the Best Practices documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full documentation set.

This is our recommended workflow for calling variants in DNAseq data from cohorts of samples, in which steps from data processing up to variant calling are performed per-sample, and subsequent steps are performed jointly on all the individuals in the cohort.

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The workflow is divided in three main sections that are meant to be performed sequentially:

  • Data cleanup: from raw DNAseq sequence reads (FASTQ files) to analysis-ready reads (BAM files)
  • Variant discovery: from reads (BAM files) to variants (VCF files)
  • Evaluation: callset QC, refinement and preliminary analyses

Important note on GATK versions


The Best Practices have been updated for GATK version 3. If you are running an older version, you should seriously consider upgrading. For more details about what has changed in each version, please see the Version History section. If you cannot upgrade your version of GATK for any reason, please look up the corresponding version of the GuideBook PDF (also in the Version History section) to ensure that you are using the appropriate recommendations for your version.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Comments

  • albertoapalbertoap USAPosts: 4Member

    Hi,
    I don't know if this is the right place to post this comment, but when using Firefox (v 29.0 Linux 64 bits) the "DNAseq" and "RNAseq" buttons don't work properly and I can't get additional information for the different steps.

    It works properly using Chromium.

    Alberto

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,192Administrator, GATK Developer admin

    Thanks for reporting this bug --I'll try to get that fixed asap.

    Geraldine Van der Auwera, PhD

  • crojocrojo CaliforniaPosts: 8Member

    Just fyi: the bug reported by @albertoap still seems to exist. In case it helps....

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,192Administrator, GATK Developer admin

    @crojo, can you tell me what is your browser/platform version?

    Geraldine Van der Auwera, PhD

  • crojocrojo CaliforniaPosts: 8Member
    edited June 2014

    @Geraldine_VdAuwera‌ sure. I'm using Firefox v 29.0.1, on Mac OS X 10.7.5.

    Post edited by crojo on
  • JorgeAmigoJorgeAmigo Santiago de CompostelaPosts: 5Member

    buttons don't work neither on Firefox v30 beta on Windows 8.1 64 bits, although tabs do work perfectly and all information seems to be accessible through them.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,192Administrator, GATK Developer admin

    OK, I have a fix for this but can't apply it yet due to other pending modifications. Should be able to get this resolved next week. In the meantime, the content of these pages can be accessed directly through the forum in the GATK Documentation / Best Practices subcategories, for anyone who is completely unable to view these pages. Sorry for the inconvenience and thanks for your patience!

    Geraldine Van der Auwera, PhD

  • mmterpstrammterpstra NetherlandsPosts: 32Member

    Should be able to get this resolved next week

    @Geraldine_VdAuwera: Are the buttons still broken? Or should i update my firefox v20? Maybe both :)

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,192Administrator, GATK Developer admin

    @mmterpstra‌ Not updated yet, sorry -- ran into a couple of issues that I need to fix before pushing changes to public. Maybe consider using Chrome in the meantime :)

    Geraldine Van der Auwera, PhD

  • geoffroyGATKgeoffroyGATK INSERMPosts: 2Member

    It is still broken with Firefox 32.0.3 on Windows 7.
    Can you push changes to public?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,192Administrator, GATK Developer admin

    @geoffroyGATK Sorry, this got pushed to the backburner. I'll try to deal with it this week as we have a couple of other fixes pending.

    Geraldine Van der Auwera, PhD

  • weberATillinoiseduweberATillinoisedu Posts: 4Member

    DNAseq and RNAseq buttons are still broken - at least in Firefox 33.0 under mac OS 10.8. Since the permanent fix may be a ways off yet, here are the links to the two sections for others who prefer to work in Firefox: DNAseq and RNAseq. Hope this helps others while this is being fixed!

    Also, Firefox displays the "broken image" symbol on some of the subsections of the RNAseq pages. These don't show up when using Safari (which may simply ignore broken images).

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