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Thu 23 Apr - Fri 24 Apr 2015
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Variant Analysis with GATK

Thu 23 Apr - Fri 24 Apr 2015

  • 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 variant 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. Special attention will be given to the newest functionalities in GATK3, including joint discovery in cohorts and RNAseq analysis.
  • The workshop will last two days, with a day and a half of lectures (including many opportunities for Q&A) and one half day of hands-on training.
  • On the first day, we will explain the rationale, theory and real-life applications of our Best Practices for Variant Discovery in high-throughput sequencing data.
  • On the second day, in the morning we will cover additional topics such as the differences between whole genome vs. exome analysis, sequence data QC metrics, and how to apply GATK to non-model organisms. In the afternoon, we will hold a hands-on session in which attendees will learn to interact with the GATK tools and apply them effectively.
  • The lecture-based component of the workshop is aimed at a mixed audience of people who are new to GATK seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. The hands-on component is aimed mainly at beginners who have basic familiarity with the command line environment.
  • A draft agenda can be found here.
  • This event is sponsored by eLife.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Further details regarding eligibility criteria are available here
  • Further details regarding the charging policy are available here
  • Familiarity with the basic terms and concepts of the genomics field
  • Basic experience of command line UNIX
  • Sufficient UNIX experience might be obtained from one of the many UNIX tutorials available online.

Number of sessions: 2

# Date Time Venue Trainers
1 Thu 23 Apr 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Geraldine Van der Auwera,  Joel Thibault,  Valentin Ruano Rubio
2 Fri 24 Apr 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Geraldine Van der Auwera,  Joel Thibault,  Valentin Ruano Rubio
Topics covered
  • Variant detection for next-generation DNA sequencing
  • Data pre-processing
  • Variant discovery
  • Variant functional annotation and evaluation

The aim of this course is to familiarise the participants with variant calling data analysis methodologies using GATK


Presentations, demonstrations and practicals




Once a year

Specialized Training

Booking / availability