Tagged with #workshop
9 documentation articles | 23 announcements | 2 forum discussions



Created 2015-08-17 23:35:00 | Updated 2015-08-17 23:35:19 | 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 2015-08-14 01:57:37 | Updated 2015-08-14 01:58:03 | Tags: best-practices workshop workflow presentations
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Joel Thibault, Valentin Ruano-Rubio and Geraldine Van der Auwera presented this workshop in Edinburgh, Scotland, and Cambridge, England, upon invitation from the Universities of Edinburgh and Cambridge.

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.


Created 2015-08-14 01:50:16 | Updated 2015-08-14 01:56:56 | Tags: best-practices workshop workflow presentations
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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. 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.

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 2014-10-31 22:45:38 | Updated 2014-10-31 23:12:02 | Tags: best-practices workshop presentations
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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.


Created 2014-10-31 17:44:07 | Updated 2014-10-31 23:14:44 | Tags: workshop presentations
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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.


Created 2014-09-16 00:04:00 | Updated 2015-04-03 14:13:28 | Tags: tutorials bundle workshop
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So you're going to a GATK workshop, and you've been selected to participate in a hands-on session? Fantastic! We're looking forward to walking you through some exercises that will help you master the tools. However -- in order to make the best of the time we have together, we'd like to ask you to come prepared. Specifically, please complete the following steps:

- Download and install all necessary software as described in this tutorial.

We don't always get around to using RStudio, but all others are required. Note that if you are a Mac user, you may need to install Apple's XCode Tools, which are free but fairly large, so plan ahead because it can take a loooong time to download them if your connection is anything less than super-fast.

- Download one of the following tutorial bundles from our FTP server:

  • The basic tutorial data bundle
    Speaking of long downloads, this one is also pretty big (740M), so again, don't leave it until last minute. This mini-bundle contains chromosome 20 of the human genome reference, a BAM file snippet and accompanying dbsnp + known indels files.

  • OR the advanced tutorial data bundle.
    If you are attending an advanced hands-on session, you'll need some extra files that aren't in the basic tutorial bundle. This add-on bundle is also quite large (870M) because it contains the complete human genome and a complete whole-genome callset. Note that this will take around 4G of space on your hard drive once it's uncompressed, so make sure you have plenty of space available on your machine.

At the start of the session, we'll give you handouts with a walkthrough of the session so you can follow along and take notes (highly recommended!).

With that, you should be all set. See you soon!


Created 2013-10-25 16:35:32 | Updated 2014-10-31 23:13:13 | Tags: best-practices workshop presentations videos
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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.


Created 2013-08-13 07:37:07 | Updated 2014-10-31 23:13:24 | Tags: official best-practices workshop
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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.


Created 2013-01-05 01:17:21 | Updated 2014-10-31 23:13:36 | Tags: best-practices workshop presentations videos
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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.


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:

https://drive.google.com/folderview?id=0BwTg3aXzGxEDVk5RcEF3WW1SQWM&usp=sharing


Created 2015-04-19 15:47:54 | Updated 2015-04-21 23:52:33 | Tags: best-practices workshop presentations topstory
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The presentation slides from the 2015 "GATK in the UK" workshop (April 20-24) are available on DropBox here.

All slides will ultimately be posted in the Presentations section of the Guide.


Created 2015-03-19 01:07:03 | Updated 2015-04-19 15:41:46 | Tags: workshop presentations topstory
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The slides from the 2015 BroadE GATK Best Practices workshop presentations are accessible at this Dropbox link.

The video recordings of the workshop talks are online here. 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.


Created 2015-02-23 21:13:29 | Updated 2015-04-02 07:31:25 | Tags: best-practices workshop
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Registration is now LIVE for our upcoming BroadE Workshop: Best Practices for Variant Calling with the GATK.

WHEN: Thursday, March 19 & Friday, March 20, 2015

10:00 AM - 5:00 PM (Lecture, March 19)
2:00PM - 5:00 PM (Optional Tutorial, March 20)

WHERE: Broad Institute

Auditorium (lecture)/Yellowstone (Tutorial)
415 Main Street
Cambridge, Massachusetts 02142

Registration Schedule:

Registration closes February 27 at 5:00 PM.
Notification of acceptance or wait list status sent by March 4.

REGISTER HERE


This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. The GATK development team and invited guests will give talks explaining the rationale, theory and real-life applications of the Best Practices. You will 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.

An optional hands-on session will be available to select participants. In this session, the GATK team will help beginners work through interactive exercises and tutorials to learn how to use GATK and apply the Best Practices to real data.

Workshop attendees will gain broad insight into the rationale of the GATK Best Practices for variant discovery, as well as a solid understanding of how individual GATK tools work and how to apply them in practice. Novices to the GATK will come out of the workshop knowing enough to identify which questions they can use address using GATK tools, how to get started on designing their experiment and analytical workflow, and how to run the tools on their own computer. Existing GATK users will come out with a deeper understanding of how the GATK works under the hood and how to improve their results further, especially as regards the latest innovations.


Created 2015-02-11 00:28:15 | Updated 2015-02-11 00:33:29 | Tags: workshop topstory
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We're going to be doing two back-to-back workshops in Edinburgh and Cambridge (the original, accept no substitutes) later this Spring, on April 20-21 and 23-24 respectively. The workshop program for both will be our typical one-day Best Practices lectures marathon followed by a half-day of lectures on supplemental topics (QC, non-humans, etc) and a half-day hands-on sessions for beginners to get their hands dirty with some real data.

These workshops are organized locally by the inviting institutions, University of Edinburgh and University of Cambridge, so please see the respective links for registration information.

Cheers to our hosts and we hope to see lots of you there!

bonus points to whoever gets the title reference -- and sings it in the correct tune


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 2014-08-28 13:44:35 | Updated 2014-08-28 13:46:08 | Tags: best-practices workshop topstory
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Here is the official announcement for the upcoming workshop in Philadelphia. Registration is not necessary for the lecture sessions, but it is required for the hands-on sessions (see link further below).

We look forward to seeing you there!


The Center for Genetics and Complex Traits (CGACT) and the Institute for Biomedical Informatics (IBI) of the University of Pennsylvania Perelman School of Medicine announce a Workshop on Variants Discovery in Next Generation Sequence Data on September 18 and 19, 2014.

This workshop will focus on the core steps involved in calling variants with the Broad Institute¹s Genome Analysis Toolkit (GATK), using the "Best Practices" developed by the GATK team, and will be presented by Dr. Geraldine Van der Auwera of the Broad Institute and other instructors from the GATK team. Participants will 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 their dataset. 

The workshop will take place over two consecutive days (September 18 and 19, 2014). In the morning lecture sessions, attendees will learn the rationale, theory, and real-life applications of GATK Best Practices for variant discovery in high-throughput DNA sequencing data, including recommendations for additional experimental designs and datatypes such as RNAseq. In the afternoon hands-on sessions, attendees will learn to interact with the GATK tools and apply them effectively through interactive exercises and tutorials.

The morning lecture sessions will take place on Thursday, September 18, from 9:00 am to 12:30 pm, and Friday, September 19, from 9:00 am to 11:30 am, in the Dunlop Auditorium of Stemmler Hall, University of Pennsylvania, 3450 Hamilton Walk, Philadelphia, PA 19104. Both morning sessions are open to all participants and registration is not required.

The afternoon hands-on sessions will take place on Thursday, September 18, from 2:00 pm to 5:30 pm, and Friday, September 19, from 1:00 pm to 4:30 pm. The September 18 hands-on session is aimed mainly at beginners (though familiarity with the command line environment is expected). The September 19 hands-on session is aimed at more advanced users who are already familiar with the basic GATK functions. Attendance to the hands-on sessions is limited to 20 participants each day, and precedence will be given to members of the University of Pennsylvania or its affiliated hospitals and research institutes (HUP, CHOP, Monell, Wistar, etc.).

Registration for the hands-on sessions is mandatory and open through Friday, August 29th at http://ibi.upenn.edu/?p=996. 

 


Created 2014-07-02 20:04:09 | Updated 2014-11-12 20:49:45 | Tags: workshop conferences meetings talks
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Ladies, gentlemen and everyone else (this is a judgment-free zone), it's officially summertime in the norther hemisphere. Depending on who and where you are, this can mean no more classes, no more exams, and more quality time with your loved ones -- or extra expense getting someone to keep your offspring out of your way (hello summer camp). It is that hallowed time of year when academics put down the burdens of teaching and administrative duties and can finally get some science done. For many, it also means conference season, e.g. meeting up in Spain with a bunch of colleagues to argue about obscure methodological details over many a glass of tinto de verano. It's a hard, hard life.

A group of us just got back from sunny Belgium* where we held a GATK workshop at the invitation of the Royal Institute for Natural Sciences in Brussels. Now we're looking ahead to the next big dates on the horizon, and I thought I'd share them here in case some of you can join us. Or in case you would like to invite us over to give talks or workshops... (seriously, private-message me if you're interested in hosting a GATK workshop).

* This is not irony, it was really beautiful the whole time. Until the two non-Belgians left, and then boom! Downpour for three days. Typical.

As you can see below, our dance card is all clear for the summer itself but starting September it gets pretty busy.


- Genome Science 2014 -- Oxford, UK, September 1-3

I will be attending the Genome Science meeting in Oxford, UK, and giving a talk in the Bioinformatics Infrastructure session.

- CppCon -- Bellevue, WA, US, September 7-12

Mauricio Carneiro and David Roazen will be attending this C++ development conference, and Mauricio will be presenting a talk titled "Gamgee: A C++14 library for genomics data processing and analysis". What this means for GATK-based development, well... happy speculating :)

- GATK Best Practices workshop -- Phildadelphia, PA, US, late September

The Center for Genetics and Complex Traits (CGACT) and the Institute for Biomedical Informatics (IBI) of the University of Pennsylvania Perelman School of Medicine are hosting our workshop. The workshop crew will consist of Eric Banks, Sheila Chandran and myself. See this announcement for more details.

- ASHG 2014 -- San Diego, US, October 18-22

Ami Levy-Moonshine will be attending the ASHG meeting in San Diego, California, and giving a compressed version of our Best Practices workshop on Tuesday 10/21 (separate registration required). Ami will also represent us in the iSeqTools workshop on cloud-based analysis on Monday10/20.

- GATK Best Practices workshop -- Cambridge, MA, US, late October/ early November

Due to scheduling constraints, we were unable to make this workshop happen, but we have tentative dates for March 2015 (3/19-3/20).


This list will be updated with any new events up to December 2014.


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:

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.


Created 2014-06-11 20:34:05 | Updated 2014-06-11 20:34:51 | Tags: best-practices workshop topstory brussels belgium
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Calling all Belgians! (and immediate neighbors)

In case you didn't hear of this through your local institutions, I'm excited to announce that we are doing a GATK workshop in Belgium in two weeks (June 24-26 to be precise). The workshop, which is open and free to the scientific community, will be held at the Royal Institute of Natural Sciences in Brussels.

This is SUPER EXCITING to me because as a small child I spent many hours drooling in front of the Institute Museum's stunningly beautiful Iguanodons, likely leaving grubby handprints all over the glass cases, to the shame and annoyance of my parents. I also happen to have attended the Lycee Emile Jacqmain which is located in the same park, right next to the Museum (also within a stone's throw of the more recently added European Parliament) so for me this is a real trip into the past. Complete with dinosaurs!

That said, I expect you may find this workshop exciting for very different reasons, such as learning how the GATK can empower your research and hearing about the latest cutting-edge developments that you can expect for version 3.2.

See this website or the attached flyer for practical details (but note that the exact daily program may be slightly different than announced due to the latest changes in GATK) and be sure to register (it's required for admission!) by emailing cvangestel at naturalsciences.be with your name and affiliation.

Please note that the hands-on sessions (to be held on the third day) are already filled to capacity. The tutorial materials will be available on our website in the days following the workshop.


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 2013-12-20 22:57:53 | Updated 2014-02-07 17:01:39 | Tags: official best-practices workshop queue presentations videos topstory
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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


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


Created 2013-09-17 18:18:29 | Updated | Tags: official best-practices workshop queue pipeline
Comments (2)

Register now for a spot at the upcoming GATK workshop, which will be held in Cambridge, MA on October 21-22.

http://www.cvent.com/events/broade-workshop-gatk-best-practices-building-analysis-pipelines-with-queue/event-summary-de1eaa027413404ba6dc04c128d52c63.aspx

This workshop will cover the following topics:

  • GATK Best Practices for Variant Detection
  • Building Analysis Pipelines with Queue

The workshop is scheduled right before ASHG Boston, so if you're going to be in town for the conference, make sure you come a couple of days early and attend the GATK workshop!


Created 2013-08-15 16:11:41 | Updated | Tags: official workshop
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We're planning the next GATK workshop to fall right before the ASHG conference in Boston, so that ASHG attendees traveling in from out of town can kill two birds with one stone.

Program details will follow, but roughly, we'll have one full day of talks devoted to the Best Practices workflow (Monday 21st) and one morning of talks devoted to pipelining analyses with Queue (Tuesday 22nd), plus an optional hands-on session on Tuesday afternoon. Registration for the talk sessions will be open to all, but the hands-on session will be reserved for Broadies.

All workshop materials will be posted online as usual of course.


Created 2013-07-09 15:54:20 | Updated 2013-08-15 16:14:59 | Tags: official best-practices workshop presentations
Comments (1)

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.


Created 2013-07-09 13:26:11 | Updated 2013-07-17 01:59:08 | Tags: tutorials official workshop
Comments (1)

Before the workshop, you should run through this tutorial to install all the software on your laptop:

We use a small test dataset that you can download from this link (1.1 Gb):

  • https://s3.amazonaws.com/gatk-workshop/mini-bundle.zip

During the hands-on session of the workshop, we walk through the following tutorials, with some minor modifications:


Created 2013-06-18 18:44:54 | Updated 2013-06-18 18:45:24 | Tags: official workshop
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Registration is now LIVE for BroadE Workshops: Best Practices for Variant Calling with the GATK.

BroadE Workshop: Best Practices for Variant Calling with the GATK
Tuesday, July 9 & Wednesday, July 10, 2013
9:00 AM - 12:00 PM

REGISTER HERE

This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will 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.

The workshop will last two days, divided into lecture-style sessions in the morning and optional hands-on sessions in the afternoon (note that for practical reasons, attendance at the latter will be limited). In the morning, you’ll hear from the GATK development team and invited guests, who will explain the rationale, theory and real-life applications of the Best Practices. In the afternoon, the GATK team will help you work through interactive exercises and tutorials in which you will apply the Best Practices to real datasets.

Optional: Hands-on tutorial sessions & Breakout session on XHMM and GenomeSTRiP

Broad Institute
Auditorium
7 Cambridge Center
Cambridge, Massachusetts 02142

Registration closes June 21 at 5:00 PM.

Notification of acceptance or wait list status sent June 27.


Created 2013-06-05 20:08:21 | Updated | Tags: official workshop
Comments (4)

We are organizing a user workshop on GATK Best Practices, which will take place July 9-10 at the Broad Institute in Cambridge, MA, USA.

The workshop will take the same format as last time, with lectures in the morning and hands-on tutorials in the afternoon on both days.

It will be free and open to all comers, but space at the hands-on tutorials will be limited, so be on the lookout for our announcement when registration opens. We will announce it here on the forum and by Twitter (follow us at @gatk_dev).

We regret that we are not able to offer any financial assistance for travel or lodging. However all the workshop materials will be posted online on our Events page on the GATK website, so be sure to check them out if you can't be here in person.


Created 2013-01-30 04:43:29 | Updated | Tags: official best-practices workshop videos
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These are videos of the presentations given at the GATK workshop on 4-5 Dec 2012 on "Best Practices for variant calling with the GATK".

http://www.broadinstitute.org/gatk/guide/events?id=2038


Created 2012-12-04 14:26:22 | Updated | Tags: official workshop presentations
Comments (4)

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

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


Created 2012-11-16 20:47:55 | Updated | Tags: workshop
Comments (1)

Registration for the GATK workshop (Dec 4-5) is now open to the public. Attendance for the hands-on portion of the workshop is limited so be sure to sign up soon!

http://www.regonline.com/builder/site/Default.aspx?EventID=1162708

Please note that this workshop is primarily intended for Cambridge and Boston-area users; users from further afield are welcome to come, but at this time we regretfully cannot offer any financial assistance for travel or lodging. Rest assured that we will make videos of the talks and all teaching materials available online following the workshop.


Created 2012-10-10 15:15:43 | Updated 2012-10-10 15:16:47 | Tags: workshop
Comments (12)

Hi all,

We are organizing a two-day GATK workshop to be held at the Broad Institute in Cambridge, MA on Dec 4-5 2012.

This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will 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.

The workshop will last two days, divided into lecture-style sessions in the morning and optional hands-on sessions in the afternoon (note that for practical reasons, attendance at the latter will be limited, so be sure to sign up early). In the morning, you’ll hear from the GATK development team, who will explain the rationale, theory and real-life applications of the Best Practices. In the afternoon, the GATK team will help you work through interactive exercises and tutorials in which you will apply the Best Practices to real datasets.

Registration is not yet open; we will post another announcement when it is, but be sure to save the date if you are interested in attending.

Please note that this workshop is primarily intended for Cambridge and Boston-area users; users from further afield are welcome to come, but at this time we regretfully cannot offer any financial assistance for travel or lodging. Rest assured that we will make videos of the talks and all teaching materials available online following the workshop.


Created 2014-01-23 18:23:49 | Updated | Tags: workshop
Comments (3)

Will there be a GATK Best Practices and Building Analysis Pipelines with Queue workshop in 2014? I would like to attend, and to put my attendance as part of a career development plan I am building. Thanks, Jimmy


Created 2013-08-01 00:20:31 | Updated | Tags: workshop
Comments (15)

Hi Team, I wonder whether you're planning to hold GATK workshops or user meetings before or after ASHG this year. I assume many users will make their way to Boston, and for those from far away (like myself), this would be very useful and efficient. Hope I didn't miss an announcement somewhere, searched but only found an IGV tutorial... Hopefully yours, K