GATK Workshop

The WV-INBRE Bioinformatics Core Facility will be hosting a three-day workshop on GATK Best Practices for Variant Calling at Marshall University, Nov 8-10 2017. The workshop will be presented by the Broad Institute and will include material on robust methods for calling germline and somatic variants using the Genome Analysis Toolkit (GATK), as well as material on the new Workflow Description Language (WDL) and Broad’s cloud-based analysis solutions. 

The workshop will comprise one day of lectures on November 8th, followed by two days of hands-on workshops. Attendees for the workshop should be comfortable using a Linux or Mac OS X command line and be familiar with the basic terminology of genomic variation. Attendees may either attend only the lectures, or the full 3-day workshop (the lectures are required for the hands-on training). Attendees for the hands-on portion of the workshop will need to bring a laptop running either Mac OS X or Linux.

For further information, contact the Bioinformatics Core Director, Jim Denvir (denvir at marshall dot edu).

The workshop is made possible with support from the West Virginia IDeA Network of Biomedical Research Excellence, and funding from the National Institutes for Health and the National Institute of General Medical Sciences (P20-GM103434).

Travel Information

Marshall University is located in downtown Huntington, WV. Huntington is approximately a two-hour drive from Lexington, KY, and three hours from Cincinnati, OH, Columbus, OH, Louisville, KY, or Morgantown, WV. For air travel, Huntington is served by Huntington tri-state airport (15 minutes’ drive from downtown), and Yeager airport in Charleston, WV is less than an hour’s drive. 

A block of rooms has been reserved at the Holiday Inn Express, 800 Third Avenue. To book under this block of rooms, either use this link or call 1-304-523-8880 and ask to book in the “GATK Workshop” group. The hotel is about 1.5 miles from campus and provides shuttle service to and from TriState Airport and in the local area.


Lunch will be provided at the workshop. For those staying at the Holiday Inn, there is a large number of excellent restaurants within easy walking distance of the hotel. 


(Agenda is subject to change)

Lectures (November 8): Rationale, theory and application of the GATK Best Practices for Variant Discovery in high-throughput sequencing data

Hands-on 1 (November 9, am): Germline variant discovery (SNPs + Indels)
Hands-on 2 (November 9, pm): Germline variant filtering (SNPs + Indels)

Hands-on 3 (November 10, am): Somatic variant discovery (SNPs + Indels + CNV)
Hands-on 4 (November 10, pm): Pipelining on the cloud with WDL

Workshop Requirements

Those attending the workshop will require a laptop running Mac OS X or Linux. The specific software required, and minimum hardware requirements, are listed on this GATK web page. Please note the following:

  • The last day of the workshop requires GATK4, which is still a product in beta release. This will likely be updated between now and the workshop, so you may want to check back and update the version a week or so before the workshop starts.
  • The Broad software requires Java version 1.8.0. Please note that Oracle recently released Java version 1.9, and Picard, GATK, and IGV have not been tested and likely will not run on Java 1.9. If you have installed Java 1.9 (a.k.a. “Java 9”), please make sure you also have Java 1.8.0 installed and know how to specify which version you are going to execute a jar file with.


Registration for this workshop is now closed.