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Created 2015-08-17 23:35:00 | Updated 2015-11-25 10:02:35 | Tags: best-practices workshop presentations slides

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Laura Gauthier, Yossi Farjoun and Geraldine Van der Auwera presented this workshop in Pretoria, South Africa, upon invitation from the University of Pretoria.

This workshop covered the core steps involved in calling germline and somatic 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.

Additional considerations were covered, such as 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 sets of hands-on tutorials aiming to teach basic GATK usage to new users, as well as introduce pipelining concepts using Queue.

The workshop was structured into five modules:

  • Introductory materials
  • Best Practices Phase 1: Pre-processing
  • Best Practices Phase 2A: Calling germline variants
  • Best Practices Phase 2B: Calling somatic variants
  • Best Practices Phase 3: Preliminary analyses

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.

Created 2016-01-31 22:32:46 | Updated 2016-02-01 15:07:30 | Tags: best-practices workshop presentations slides

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This week we are teaching a couple of GATK Best Practices workshops in Sydney (one Opera House, check) and Melbourne, Australia. Joining me are Methods Team developers Mark and Megan.

The presentation slides from Day 1 as well as the materials for the Day 2 hands-on tutorial are available at this Google Drive link.

Learned so far: the fierceness of the Australian sun is no laughing matter

Created 2015-12-08 08:22:39 | Updated 2015-12-09 18:42:17 | Tags: workshop presentations rnaseq slides

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The hands-on tutorial files and presentations slides from the Dec 8, 2015 workshop at VIB in Gent, Belgium are available at this link:


Created 2015-11-18 21:12:35 | Updated 2016-01-27 05:58:23 | Tags: workshop presentations slides topstory talks

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These are the materials that were presented at the November 2015 GATK workshop at the Broad Institute in Cambridge, MA.

Materials Link
Slide decks presented on Day 1 Google Drive Folder
Workshop handout document (agenda and talk abstracts) PDF on Google Drive
Variant Discovery Tutorial (Day 2 AM) (=ASHG15 Tutorial) Google Drive Folder
Callset Filtering and Evaluation Tutorial (Day 2 PM) Google Drive Folder

Created 2015-06-22 11:32:51 | Updated 2015-06-23 03:37:31 | Tags: workshop presentations slides

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The slides from the workshop presentations as well as related materials will be posted here at the end of each day:


Created 2014-09-18 04:52:29 | Updated 2014-09-22 18:26:47 | Tags: workshop presentations slides

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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.

Created 2014-09-04 13:00:58 | Updated | Tags: presentations conferences slides talks

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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.

Created 2014-06-25 03:16:27 | Updated | Tags: workshop presentations slides

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The presentation slides are available on DropBox at this link:


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

Created 2014-04-10 17:39:08 | Updated | Tags: video presentations appistry webinar slides gatk3

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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.

Created 2014-03-02 16:59:24 | Updated 2014-03-02 17:02:01 | Tags: workshop presentations slides

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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.

Created 2013-10-22 02:40:27 | Updated 2013-10-22 14:49:48 | Tags: best-practices workshop queue presentations slides

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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 :


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