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.

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Genomeo on 18 Sep 2015

Hi. Thanks for workshop. What is the link for downloading the workshop material?

ebaschal on 18 Sep 2015

I am looking forward to the workshop. Can you make sure the materials are available for download today or tomorrow morning? My flight is very early Monday morning, and I will be unable to print or download the material after that. Thank you!

Geraldine_VdAuwera on 18 Sep 2015

Sorry for the delay folks; the materials will be posted by end of day today.

Geraldine_VdAuwera on 18 Sep 2015

A Google Doc for tutorial questions is now open here: https://drive.google.com/open?id=142BLvoe-1rqh6HsLduOEdkPMF2b8PwFdpyhOpEIh5eY This is restricted to ASHG workshop attendees.

bkelly on 18 Sep 2015

For next year's ASHG, would it be possible to have a "beginners" workshop and an "advanced" workshop? I keep coming to the workshops and re-learning every year what a BAM is and what information is contained in the VCF. You would be able to get in to the weeds a little deeper than when you have to spend time going through all of the basic information.

Geraldine_VdAuwera on 18 Sep 2015

@bkelly That's a fair point. We struggle every year with how to serve as many people as we can, and we typically fall on the side of serving the beginners more because we think they need the most help to get started. We try to communicate that in our workshop description, but let us know if you feel that hasn't been the case. For sure we realize it must be frustrating for more advanced users to not get deeper information, and your suggestion makes a lot of sense to me. I would love to do that -- we're eager to get into the deeper weeds as well. The sticking point is going to be convincing the conference organizers to give us two workshop slots, when there are many other groups applying to do workshops. Perhaps we can run an unofficial workshop in parallel to the conference; we'll look into it for next time. In the meantime, do come see us after the session and hopefully we can answer some more advanced questions for you.

dfardo on 18 Sep 2015

Where will the presentation slides be posted?

Geraldine_VdAuwera on 18 Sep 2015

@dfardo I added the link to download the presentation in the article above.

dfardo on 18 Sep 2015

@Geraldine_VdAuwera Thanks! The Intro presentation slide deck link sends me to ASHG15 - GATK workshop Q&A which is "in owner's trash." Can you relink or send directly? Sorry if user error. :blush:

Geraldine_VdAuwera on 18 Sep 2015

@dfardo My bad, fixed now!

Sheila on 18 Sep 2015

@bkelly Hi, Can you tell us specifically what you would be interested in learning during an advanced workshop? Are you interested in the steps after Variant Calling, like filtering and evaluation? Or, are you interested in learning more about the pre-processing and variant calling algorithms? Thanks, Sheila

dfardo on 18 Sep 2015

@Geraldine_VdAuwera Got it -thanks!

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