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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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  • Who's (Not) Afraid of the Batch Effect Boogeyman?
    How do people deal with batch effects? Batch effects encompass all the ways t...
  • Joint Calling and the Batch Effect Boogeyman
    What happens if you don’t joint call all your samples together? Why do people...
  • Masked reference genomes
    The work presented here includes significant contributions from Pankaj Vats a...
  • Introducing GATK "Biggest Practices" for Joint Calling Supersized Cohorts
    DNA sequencing continues to get cheaper and cheaper as time goes on, which me...
  • ⚙️ GATK 4.3 release
    The latest GATK release came out a few weeks ago, with changes corresponding...
  • Introducing NVIDIA's NVScoreVariants, a new deep learning tool for filtering variants
    If you know only one thing about NVIDIA, it's probably that they manufacture...
  • Hacking GATK to reduce your cloud costs
    When it comes to research, time is money. And that couldn't be any more liter...
  • GenotypeGVCFs and the death of the dot (obsolete as of GATK 4.6.0.0)
    ⚠️ NOTE ⚠️ This article describes behavior present in GATK versions 4.2.3.0 t...
  • Please update your GATK - Important information about GATK 4.2.6.1
    🚨 If you are using GATK version 4.2.5.0, please update to the newest releas...
  • GATK on the cloud, with Terra
    We've talked about Terra here before, but we thought it might be useful to re...
  • Important: GATK version update required to address Log4j security vulnerability
    We have an important update regarding the safety of running GATK. As you may ...
  • Full release of open-source DRAGEN-GATK 1.0
    It's finally here! We've been talking about it (on the old, now archived blog...
  • Introducing DRAGMAP, the new genome mapper in DRAGEN-GATK
    As you may know from previous posts, we’ve been working with the DRAGEN team ...
  • ⚙️ GATK 4.2.3.0 release
    The latest GATK release is out, with changes corresponding to the period of ...
  • ⚙️ GATK 4.2.2.0 release
    The latest GATK release is out, with changes corresponding to the period of ...
  • ⚙️ GATK 4.2.1.0 release
    The latest GATK release is out, with changes corresponding to the period of ...
  • Introducing GATK for Microbes
    Being able to accurately identify mutations in microbial genomes is an essent...
  • From GATK 4.1 to 4.2: Two years of updates in a nutshell
    It’s been over two years since we released GATK 4.1, so now is definitely the...
  • ⚙️ GATK 4.2 release
    The latest GATK release is out, with changes corresponding to the period of ...
  • New Year update — GATK takes on 2021
    Well folks, this new year is off to a heck of a start. I don't know who needs...
  • ⚙️ GATK 4.1.9.0 release
    The latest GATK release is out, with changes corresponding to the period of ...
  • Mutect2 Webinar Announcement and A Call for Questions From Our Community
    Do you miss the in-person GATK workshops we used to host back in pre-pandemic...
  • DRAGEN-GATK update: Upcoming webinar and pipeline release timeframe
    A year ago this month, we announced the start of our collaboration with the D...
  • Downsampling in GATK
    By Takuto Sato, Computational Methods Team, Data Sciences Platform __________...
  • ⚙️ GATK 4.1.8.0 release
    The latest GATK release is out, with changes corresponding to the period of ...
  • Genomics in the Cloud: Origins
    In my last blog post, I introduced the book that Brian O'Connor and I recentl...
  • Introducing Genomics in the Cloud, ie "The GATK book"
    I always wince a bit at the phrase "we are thrilled to announce bla bla blah"...
  • Detecting sample swaps with Picard tools
    By Yossi Farjoun, Associate Director of computational research methods in the...
  • GATK Workshops: Cancellations & Rescheduling
    In light of recent developments regarding the ongoing COVID-19 outbreaks, we...
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