created by Geraldine_VdAuwera
on 2015-10-27
As announced recently, we are doing a workshop at the Broad Institute in Cambridge this coming November 18-19 (description below the fold).
Registration for the workshop is now live here.
Registration will close Oct. 30 (this Friday) so don't wait to sign up!
Workshop attendees will gain broad insight into the rationale of the GATK Best Practices for variant discovery, as well as a solid understanding of how individual GATK tools work and how to apply them in practice. Novices to the GATK will come out of the workshop knowing enough to identify which questions they can address using GATK tools, how to get started on designing their experiment and analytical workflow, and how to run the tools on their own computer. Existing GATK users will come out with a deeper understanding of how the GATK works under the hood and how to improve their results further, especially with respect to the latest innovations.
The workshop consists of an all day lecture series and two optional hands-on tutorials on the second day.
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. The GATK development team and invited guests will give talks explaining the rationale, theory and real-world applications of the Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are 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 lecture topics include somatic variant calling with MuTect2 and somatic copy number variant calling.
One of two optional hands-on tutorials will be available to select participants. In each tutorial, the GATK team will guide participants in applying GATK tools on provided example data. The two sessions reflect different stages of research—data generation versus evaluation of results. The morning session is titled Joint Variant Discovery, and participants will come out knowing how to use the GVCF workflow and how to interpret results. The afternoon session is titled Variant Callset Filtering and Evaluation, and participants will come out knowing how to use tools to evaluate and filter a variant callset. Tutorial attendees must bring their own LINUX or Mac laptop and be able to install software according to provided instructions. Please note if you choose to follow the tutorial on a server requiring Wi-Fi; we cannot provide support during the session.