If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
GATK workshop at ASHG 2015
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:
- Intro presentation slide deck
- 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 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
- Open the
ASGH15_GATKdirectory, look at the contents and read the extremely brief
Refresh your memory of the topic and scientific context of the workshop: 10-20 minutes
- Open the PDF document called
- 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.