Tagged with #presentations
7 documentation articles | 12 announcements | 1 forum discussion


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Ami Levy-Moonshine presented this condensed 90-minute workshop given at ASHG 2014 in San Diego, CA on October 21.

This workshop covered all the core steps involved in calling variants with the GATK, using the “Best Practices” developed by the GATK team. The presentation materials outline why each step is essential to the calling process and what are the key operations performed on the data at each step. This includes specific information about variant calling in RNAseq data and efficient analysis of cohorts.

His slide deck is available at this link if you're viewing this post in the forum, or below if you are viewing the presentation page already.

GATK was also featured in another mini-workshop at ASHG which covered the iSeqTools network, focused on cloud-based analysis. The presentation slides will be posted to the iSeqTools website in the near future.

Best Practices for variant discovery in DNA:

Best Practices for variant discovery in RNAseq:

Excerpt from Ami's ASHG poster:

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Eric Banks, Sheila Chandran and Geraldine Van der Auwera presented this workshop in Philadelphia, PA, upon invitation from the School of Medicine at UPenn.

This workshop covered all the core steps involved in calling variants with the GATK, 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. This includes specific information about variant calling in RNAseq data and efficient analysis of cohorts.

The material was presented over two days, organized in the following modules:

  • Data pre-processing: From FASTQ to analysis-ready BAM
  • Variant Discovery: From BAM to analysis-ready VCF

This was complemented by a set of hands-on exercises aiming to teach basic GATK usage to new users.

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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Mauricio Carneiro presented this talk at CPPCON (C++ conference) in Bellevue, WA on September 8, 2014. His slide deck and a link to the video are available at this link if you're viewing this post in the forum, or below if you are viewing the presentation page already.

Abstract

Our group has defined the standards for DNA and RNA sequencing data processing and analysis for disease research and clinical applications. In the last 5 years we have published our tools in the GATK (genome analysis toolkit) which is completely written in java. With the scaling of next generation sequencing and the immense amount of that needs to be processed we hit a performance wall and found ourselves limited by the language to make optimizations and rewrite the algorithms in a way that would conform better to modern hardware.

Enter Gamgee. A free and open source C++14 library that offers much of the functionality of the GATK framework with the performance necessary to scale to the hundreds of petabytes of todays complex diseases projects. We will show how the tools developed using the Gamgee library replaced legacy java GATK tools in the production pipeline of the Broad Institute. We will also talk about how the algorithms have changed to take advantage of the native libraries and modern hardware features such as SSE/AVX and GPUs.

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Laura Gauthier, David Roazen and Geraldine Van der Auwera presented this workshop in Brussels, Belgium, upon invitation from the Royal Belgian Institute for Natural Sciences.

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. 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.

  • Beyond the Best Practices

    Additional considerations such as calling variants in RNAseq data and calling cohorts efficiently, as well as dealing with non-human data, RNAseq data, whole-genome vs. exome, basic quality control, and performance.

This was complemented by a set of hands-on exercises aiming to teach basic GATK usage to new users.

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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Mauricio Carneiro presented this slide deck at the workshop organized by Mnt Sinai School of Medicine on December 10, 2013. The other presentations made at the workshop were posted here.

Please note that we cannot guarantee content hosted on other websites; if outgoing links becomes outdated please let us know.

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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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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. 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.

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The slide from the 2015 BroadE GATK Best Practices workshop presentations are accessible at this Dropbox link.

The video recordings of the workshop talks will be online in a few weeks. We'll post links to the videos (along with copies of the corresponding slides) in the Presentations section of the Guide. They will also be available on the Broad's YouTube and iTunesU channels.

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The presentation slides for Day 1 of the workshop are available online here.

EDIT -- Day 2 materials are also available at the link above.

EDIT -- Hands-on materials also added above.

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The slides from the talk I gave at the Genome Science UK conference (Oxford, Sept 2) are now available here.

A few impressions below the fold.


As always it was fun meeting plenty of GATK users and other researchers in general, and very exciting to get to spread the word about our new workflow and the HaplotypeCaller's capabilities. Special thanks to Mick Watson from Edinburgh Genomics for inviting me, and his team for making me feel super welcome.

I really enjoyed getting to see quite a few microbial genomics talks, since I am originally a microbiologist by training. Too bad I had to miss the plant/forestry B session, as I'm very curious about the crazy-ploidy aspects of plant genomics, but that's the curse of parallel sessions I suppose. Very interesting conference overall for sure, and a nice group size -- lively but not overwhelming (I dislike mega-cons like ASHG). Though maybe next time Nick Loman should get the main lecture theater for his MinION talk instead of the little basement room -- and someone should make sure the wifi network can handle dozens of data-crazed scientists trying to download his MinION datasets at the same time.

A final note on the live-tweeting, i.e. people in the audience tweeting snippets during the talk. I was aware of this as a trend, and in fact I've followed tweet-streams of other people's talks, but had never experienced it myself as a speaker. It's a bit nerve-inducing but very interesting as an insight into what (at least some of) the audience reacted most strongly to and took away from the talk. It also stimulated some interesting follow-up exchanges, so I'll tentatively classify it as a Good Thing for now.

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The presentation slides are available on DropBox at this link:

https://www.dropbox.com/sh/rc1fdwet00bzq1v/AADjIpO8tE4HSKmCB2Kq1zlIa

After the workshop, these materials as well as the hands-on tutorial will be posted in the Presentations section of the website.

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The slides from today's webinar are available as of now in the GSA team Dropbox at this link, and will be on the documentation website shortly.

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This week, three lucky GATK team members are teaching an invited workshop at Mahidol University in Bangkok, Thailand! The slide decks for each day will be available at the start of the day here in the GSA dropbox. After the workshop, all materials will be available in the Presentations section of the GATK website as usual.

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The presentation videos for:

  • Day 1 (Best Practices for Variant Calling with GATK)
  • Day 2 (Building Analysis Pipelines with Queue)

are available here: http://www.broadinstitute.org/gatk/guide/events?id=3391

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Slides for :

  • Day 1 (Best Practices for Variant Calling with GATK)
  • Day 2 (Building Analysis Pipelines with Queue)

are available at this link in our DropBox slide archive :

https://www.dropbox.com/sh/ryz7bx4aeqc7mkl/44Q_2jvIyH

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The slides from the July 2013 Best Practices workshop are available here:

https://www.dropbox.com/sh/jhlk451jntywfdy/vJqbKTZZd_

The videos will be put online once they are processed.

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Hi everyone,

The slides of the presentations that Mark DePristo and Mauricio Carneiro gave at AGBT this week are online!

Please see this page:

http://www.broadinstitute.org/gatk/guide/events?id=2247

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Here is a Dropbox link to the presentations given at the Dec 4-5 GATK workshop:

https://www.dropbox.com/sh/0puyz82ecswm4ig/V2fW--1ZFS

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Hi everyone,

The GATK team recently presented a broad overview of sequencing analysis and variant calling using GATK 2.0 at the Broad Institute Medical and Population Genetics Program meeting. This slides are a great introduction to all the latest improvements in the GATK that are in version 2.0.

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Hi,

I recall in the old gatk introduction page, there is a link to a page (drop box?) that contains all presentation slides for 2010 and 2011 workshop slides and some other presentation slides. I could not find the link now. Could you point me to the URL location?

Thanks in advance for your help.

-XZ