Tagged with #workshop
9 documentation articles | 33 announcements | 2 forum discussions



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 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
Comments (2)

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
Comments (7)

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: 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 2016-02-12 01:18:16 | Updated | Tags: best-practices workshop
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For the last few years, we have taught GATK workshops at institutions in various countries around the world. It started out as a small-scale effort with one or two workshops a year in addition to the annual workshop hosted at the Broad itself, but it seems that word has gone around because our dance card is filling up faster every year. Here's a quick recap of where we stand for the 2016 season.


The tour so far

We kicked off this year's World Tour in style -- on the other side of the world! In two back-to-back 2-day workshops in Sydney and Melbourne, our 3-person workshop crew walked a diverse assortment of researchers and bioinformaticians through the essentials of GATK Best Practices for Variant Discovery, in theory on Day 1 and in practice on Day 2. Lots of great questions were asked, most were answered, and a lot of coffee was consumed. Our thanks to Bioplatforms Australia for setting up these workshops at UNSW in Sydney and at the University of Melbourne, and taking great care of us (so much good coffee!). We look forward to hearing from our Aussie users on the forum.


Upcoming locations/dates

We have more workshops coming up in the US and in Europe, and registration is open for some of them! Here's the list up to June:

  • March 2-4: Los Angeles, USA (UCLA) -- register here
  • April 14-15: Edinburgh, UK (University of Edinburgh) -- register here
  • April 18-19: Oxford, UK (University of Oxford)
  • June 13-14: Cambridge, UK (University of Cambridge) -- register here
  • June 16-17: Helsinki, Finland (CSC-IT Center for Science)

Remaining registration links will be added when they become available.

We are looking into possible workshop dates for later in the year (September - December).


What if you can't attend?

If you can't make it to one of our workshops in person, check out the Presentations section of the documentation guide. There you can watch the workshop videos from the BroadE workshops, as well as download the workshop slides and tutorial materials from all workshops that we have taught so far. Some of the most recent haven't been posted yet but we'll get that done soon. In the meantime if you're in a hurry you can find those materials in previous posts; look for the "workshops" or "presentations" tags.


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:

https://drive.google.com/folderview?id=0BwTg3aXzGxEDb2hTWERNWHg3c2M


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 2015-11-16 07:07:45 | Updated 2015-11-19 18:09:19 | Tags: tutorial workshop
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We are scheduled to do 2 hands-on modules at the BroadE GATK workshop at the Broad Institute this Thursday, Nov. 19.

The tutorial materials for each module include the following:

  • Workshop dataset and an appendix document containing detailed instructions for preparing for the workshop
  • Tutorial worksheet containing the actual exercises done in the workshop

Attendees will receive a printout of the worksheets for the module to which they have registered. We will not provide printouts of the appendix documents.

If you are registered to attend, you must have downloaded the materials and followed the instructions before the workshop starts, otherwise you will not be able to follow along and your workshop experience will be unsatisfying. We certainly don't want that to happen, so be sure to do your homework as follows below the fold. Be sure to identify correctly which workshop you are registered for!


Variant Discovery (morning session)

Get the dataset + appendix bundle: 5 minutes

Note that the file and directory names make reference to ASHG 2015 because these materials were originally developed for the GATK workshop we taught at the ASHG 2015 meeting. There, that's one mystery cleared up!

  • Download the 52 Mb zip file to the laptop you will bring to the workshop, and save it where you want the tutorial files to sit.
  • Open the zip file; this will create a directory called ASGH15_GATK.
  • Open the ASGH15_GATK directory, look at the contents and read the extremely brief README.txt file.

Refresh your memory of the topic and scientific context of the workshop: 10-20 minutes

  • Open the PDF document called ASGH15_GATK-Appendix.
  • Read the introduction. If any of the content is especially new or confusing to you, consider following the links included to the additional documentation on our website. We will cover this content briefly at the start of the tutorial, but the more you prepare, the better your workshop experience will be.

Install and test software: 30-45 minutes

Go over the second part of the ASGH15_GATK-Appendix document to acquaint yourself with the technical requirements of the workshop and follow the detailed installation instructions. In particular:

  • Make sure you have the correct version of Java installed (Java 7 / JRE 1.7).
  • Download all 3 software packages (GATK, Samtools, IGV) to the laptop you will bring to the workshop.
  • Copy the program files of all three to the ASGH15_GATK directory.
  • Run the test commands for GATK and Samtools, and launch IGV.

If you are new to the command line or GATK, we strongly recommend reviewing the sections of the document about tool syntax (pages 8-10) and practicing basic Unix commands. You may also benefit from spending some time gaining familiarity with IGV.


Callset Filtering & Evaluation (afternoon session)

The appendix file is now available from this link. The data bundle is available here.

Be sure to have done the workshop preparation homework as outlined below and described in the Appendix!

Refresh your memory of the topic and scientific context of the workshop: 10-20 minutes

  • Open the PDF document called BroadE2015-Filtering_Tutorial-Appendix (linked above).
  • Read the introduction. If any of the content is especially new or confusing to you, consider following the links included to the additional documentation on our website. We will cover this content briefly at the start of the tutorial, but the more you prepare, the better your workshop experience will be.

Install and test software: 30-45 minutes

Go over the second part of the BroadE2015-Filtering_Tutorial-Appendix document to acquaint yourself with the technical requirements of the workshop and follow the detailed installation instructions. In particular:

  • Make sure you have the correct version of Java installed (Java 7 / JRE 1.7).
  • Download all software packages listed (GATK, RStudio, IGV) to the laptop you will bring to the workshop.
  • Create a directory called BroadE2015 where you will put tutorial files.
  • Copy the program files of all three to the BroadE2015 directory.
  • Run the test commands for GATK and RStudio/ggplot, and launch IGV.

If you are new to the command line or GATK, we strongly recommend reviewing the sections of the document about tool syntax (pages 8-10) and practicing basic Unix commands. You may also benefit from spending some time gaining familiarity with IGV and RStudio.


Created 2015-10-27 00:52:01 | Updated | Tags: workshop
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As announced recently, we are doing a workshop at the Broad Institute in Cambridge this coming November 18-19 (description below the fold).

Registration for the workshop is now live here.

Registration will close Oct. 30 (this Friday) so don't wait to sign up!


Overview

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 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 with respect to the latest innovations.

The workshop consists of an all day lecture series and two optional hands-on tutorials on the second day.

Day 1 - Lecture

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-world applications of the Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are 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.

Special lecture topics include somatic variant calling with MuTect2 and somatic copy number variant calling.

Day 2 - Hands-on Tutorials

One of two optional hands-on tutorials will be available to select participants. In each tutorial, the GATK team will guide participants in applying GATK tools on provided example data. The two sessions reflect different stages of research—data generation versus evaluation of results. The morning session is titled Joint Variant Discovery, and participants will come out knowing how to use the GVCF workflow and how to interpret results. The afternoon session is titled Variant Callset Filtering and Evaluation, and participants will come out knowing how to use tools to evaluate and filter a variant callset. Tutorial attendees must bring their own LINUX or Mac laptop and be able to install software according to provided instructions. Please note if you choose to follow the tutorial on a server requiring Wi-Fi; we cannot provide support during the session.


Created 2015-10-23 21:13:17 | Updated | Tags: workshop
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Yay, it's workshop planning season again!

USA: Cambridge, MA - November 18-19, 2015

Another local BroadE workshop at the Broad Institute for our Boston Metro Area peeps (and anyone who cares to travel to us on short notice). This will be the last workshop of 2015 and the first to cover the upcoming GATK version 3.5 -- which we really have to release soon now! As usual, the topic will be GATK Best Practices, with all the latest updates, some fresh material including two somatic variant discovery talks, and two completely revamped hands-on tutorial sessions. Registration will open on Monday, October 26 and stay open for one week. We'll post a link to the registration site when it goes live.

More below the fold: our preliminary workshop lineup for the 2016 Winter & Spring season.


Specific details per workshop to be announced as they become available. Dates are given as an estimate pending confirmation (some workshop plans are still subject to changes by the organizing hosts).

Australia: Sydney and Melbourne - February 1-5, 2016

2x Two times two-day Best Practices workshops back to back in Sydney and Melbourne. Pick your city, Aussies. Kiwis welcome, although we'd prefer if you invited us over to you at some point as well ;)

USA West Coast: LA - March 2-4, 2016

Three-day workshop with morning talks and afternoon hands-on tutorials at UCLA. We're looking forward to visiting the Walk of Fame.

UK: Oxford and possibly Edinburgh - April 14-19, 2016

2x Two-day Best Practices workshops back to back. Pick one.

If you're at U of Edinburgh, there's currently a survey going around to gauge interest in doing another workshop (we did one earlier this year). Find it and let them know you want it to happen.

Oxford, we're definitely coming to you.

UK and Finland: Cambridge and Helsinki (?) - June 13-17, 2016

2x Two-day Best Practices workshops back to back. Pick one.

Perhaps not the most obvious pairing, but there we go. Literally. We're going there.

And yes, that's the original Cambridge.

[Your country and institution here]

In case you're wondering: we're open for invitations by academic and non-profit organizations for any month of 2016 not already booked. We don't charge for giving the workshops; we just ask for the inviting host to cover our travel and living costs.

Note: if you're a commercial organization interested in on-site training opportunities, let us know by email at softwarelicensing@broadinstitute.org and our business office will be in touch to discuss options.


Created 2015-10-08 19:05:57 | Updated | Tags: workshop poster ashg
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Great poster session this morning at ASHG; Sheila and I got a lot of good questions about the Best Practices, and the GVCF workflow in particular. Our punchline: "This is how ExAC got done". It's super effective!

Preview of the poster after the fold. You can get the full-sized PDF here.



Created 2015-10-04 07:15:53 | Updated | Tags: tutorials workshop ashg
Comments (4)

Are you excited? We sure are. Especially in the secondary sense defined by dictionary.reference.com as "stimulated to activity; brisk:". We're presenting a poster on Thursday and a 90-minute workshop on Friday, but neither is ready yet. Good thing the weather this weekend is crappy; if we were missing out on proper New England fall foliage / leaf-peeping weather we'd be pretty cheesed off.

But we ain't afraid of no deadline -- we'll be ready. We developed a completely new workshop tutorial for the occasion, and we're going to have a big room full of people rocking GVCFs. It's going to be epic. The tutorial data bundle, sans worksheet (because that's the part that's not quite ready yet) is already available here (not a direct link to the data because we want you to read the part about the homework). It does have an appendix document with installation instructions and some context info about the tutorial objectives, which you must read through (and act on) before the workshop, if you're attending.

If you're at ASHG but you can't make it to the workshop, you can still come see our poster, which covers the same topic (the GVCF workflow part of the Best Practices), but flatter and less interactive. Although Sheila and I will be there to answer questions one on one, so in that sense it will be more interactive. Just with less keyboard action. So, Thursday 9 Oct between 12 and 1 pm at the Bioinformatics and Genomic Technology session in the Exhibit Hall, Level 1; Convention Center, poster #1664/T. Be there. We'll talk.

We'll also be around at the Broad Institute Genomic Services booth in the Exhibit Hall (booth #1720, right around the corner from Qiagen). Not sure yet when we'll be there, but send me a private message if you'd like to chat and we can figure out a time.

See you there!


Created 2015-09-18 18:30:18 | Updated 2015-10-12 18:45:05 | Tags: workshop topstory ashg
Comments (13)

We are scheduled to do a hands-on workshop at the ASHG 2015 meeting in Baltimore (see below for program details).

The workshop files are available here:

Attendees will receive a printout of the worksheet at the workshop. We will not provide printouts of the appendix document.

If you are registered to attend, you must have downloaded the materials and followed the instructions before the workshop starts, otherwise you will not be able to follow along and your workshop experience will be unsatisfying. We certainly don't want that to happen, so be sure to do your homework as follows:

Get the files: 5 minutes

  • Download the 52 Mb zip file to the laptop you will bring to the workshop, and save it where you want the tutorial files to sit.
  • Open the zip file; this will create a directory called ASGH15_GATK.
  • Open the ASGH15_GATK directory, look at the contents and read the extremely brief README.txt file.

Refresh your memory of the topic and scientific context of the workshop: 10-20 minutes

  • Open the PDF document called ASHG2015Tutorial-Appendix.
  • Read the introduction. If any of the content is especially new or confusing to you, consider following the links included to the additional documentation on our website. We will cover this content briefly at the start of the tutorial, but the more you prepare, the better your workshop experience will be.

Install and test software: 30-45 minutes

Go over the second part of the ASHG2015Tutorial-Appendix document to acquaint yourself with the technical requirements of the workshop and follow the detailed installation instructions. In particular:

  • Make sure you have the correct version of Java installed (Java 7 / JRE 1.7).
  • Download all 3 software packages (GATK, Samtools, IGV) to the laptop you will bring to the workshop.
  • Copy the program files of all three to the ASGH15_GATK` directory.
  • Run the test commands for GATK and Samtools, and launch IGV.

If you are new to the command line or GATK, we strongly recommend reviewing the sections of the document about tool syntax (pages 8-10) and practicing basic Unix commands. You may also benefit from spending some time gaining familiarity with IGV.


Interactive Invited Workshop: Latest and Greatest Innovation in Variant Discovery with GATK

Room 343, Level 3; Convention Center
7:15am - 8:45am
Fri, Oct 09

Accredited session: 1.5

By invitation or pre-registration only

The Genome Analysis Toolkit or GATK, developed at the Broad Institute, is currently one of the most widely used software tools for variant discovery and genotyping in whole genome and exome data. This workshop will present the core “Best Practices” developed by the GATK team, which are crucial to getting the most accurate and meaningful results out of any variant discovery analysis. The Best Practices workflow is a complete solution for variant discovery that goes from data preparation to variant calling and filtering. We will focus especially on the latest methodological innovations that can enable researchers to obtain best-in-class results from their data. We will cover the underlying principles of the methods that are utilized, as well as how to apply them in practice, demonstrating usage and walking attendees through the process on a real data set. The workshop will include a “hands-on” component (involving a downloadable test data set and course materials) so that attendees who wish to do so can follow along and run the commands themselves on their laptop. In addition to the principal instructor, teaching assistants will be available to answer questions during the hands-on parts. Through this workshop, attendees will be empowered to leverage the power of GATK and apply our Best Practices variant discovery workflow in their own research.

Workshop requirements: You must bring your laptop. Your laptop should have full battery power and must have a wireless card.

To attend this event, a separate ticket must be purchased during the meeting registration process. Limited tickets are available and sell out early. Tickets will not be available for sale on site. Registration cost includes breakfast.


Created 2015-06-22 11:32:51 | Updated 2015-06-23 03:37:31 | Tags: workshop presentations slides
Comments (0)

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
Comments (1)

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
Comments (0)

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
Comments (8)

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
Comments (2)

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
Comments (1)

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
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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: 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
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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: 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: workshop
Comments (3)

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: 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 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):

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: 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: 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: best-practices workshop videos
Comments (0)

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: 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