Organizer: University of Cambridge

Host institution: University of Cambridge Bioinformatics Training

Start: Thursday, 23 April 2015 @ 08:30

End: Friday, 24 April 2015 @ 16:30

Venue: Craik-Marshall Building

City: Cambridge

Country: United Kingdom

Postcode: CB2 3AR

Target audience:
  • Graduate students
  • Postdocs and Staff members from the University of Cambridge
  • Institutions and other external Institutions or individuals
Description:

*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.''

Event type:
  • Workshops and courses

Keywords: HDRUK

Variant Analysis with GATK https://tess.elixir-europe.org/events/variant-analysis-with-gatk-2aa6f7c8-24d5-4427-bb1c-cfb82494bb71 *This workshop will focus on the core steps involved in calling variants with the Broad’s [Genome Analysis Toolkit](https://www.broadinstitute.org/gatk/), 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](https://drive.google.com/file/d/0B5BzNXp93Gp5eWtiaWtFdnJRcEU/view?usp=sharing). * This event is sponsored by [eLife](http://elifesciences.org/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://marstons.bio.cam.ac.uk/course-booking/?CourseID=Bioinformatics:%20Variant%20Analysis%20with%20GATK%20_2015.04.23-24_1380452&CourseName=Bioinformatics:%20Variant%20Analysis%20with%20GATK&CourseDate=2015.04.23-24&CourseDuration=2&EventID=1380452).'' 2015-04-23 08:30:00 UTC 2015-04-24 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK