BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260809T003724Z UID:d992fea0-4132-41d2-83e6-ef1a4709c9dc DTSTART:20190708T083000Z DTEND:20190711T153000Z DESCRIPTION:This workshop will focus on the core steps involved in calling germline short variants\, somatic short variants\, and copy number alterat ions with the [Broad’s Genome Analysis Toolkit (GATK)](https://www.broad institute.org/gatk/)\, using “Best Practices” developed by the GATK me thods development team. A team of methods developers and instructors from the Data Sciences Platform at Broad will give talks explaining the rationa le\, theory\, and real-world applications of the GATK Best Practices. You will learn why each step is essential to the variant-calling process\, wha t key operations are performed on the data at each step\, and how to use t he GATK tools to get the most accurate and reliable results out of your da taset. If you are an experienced GATK user\, you will gain a deeper unders tanding of how the GATK works under-the-hood and how to improve your resul ts further\, especially with respect to the latest innovations.\n\n\n*Day 1: Introductory and Overview. The first day of the workshop gives a high- level overview of various topics in the morning\, and in the afternoon we show how these concepts apply to a case study. The case study is tailored based on the audience\, as represented by their answers in our pre-worksho p survey.\n\n \n*Day 2: Germline Short Variant Discovery. Today we dive d eep into the tools that make up the GATK Best Practices Pipeline. In the m orning we discuss variant discovery\, and in the afternoon we look at refi nement and filtering. You will have the opportunity both in the morning an d in the afternoon to get hands-on with these tools and run them yourself. \n\n*Day 3: Somatic Variant Discovery. Today we will cover Somatic Varian t Discovery in more depth. In the morning we primarily focus on calling sh ort variants with Mutect2\, and in the afternoon we look at copy number al terations. Both sections have a paired hands-on activity.\n\n*Day 4: Pipe lining. Over the first three days\, you would have learned a lot about dif ferent pipelines and tools that you can use in GATK. Today we will be lear ning all about how those pipelines are written in a language called WDL. I n the afternoon we cover other useful topics to working on the cloud\, inc luding Docker and BigQuery.\n\nPlease note that this workshop is focused o n human data analysis. The majority of the materials presented does apply equally to non-human data\, and we will address some questions regarding a daptations that are needed for analysis of non-human data\, but we will no t go into much detail on those points.\n\nThe hands-on GATK tutorials in t his workshop will be conducted on [Terra](https://terra.bio/)\, a new plat form developed at Broad in collaboration with Verily Life Sciences for acc essing data\, running analysis tools and collaborating securely and seamle ssly.\n\nThe training room is located on the first floor and there is curr ently no wheelchair or level access available to this level.\n\nPlease not e 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 re gister Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/boo king-form/?event-id=2858057&\;course-title=Variant%20Discovery%20with%2 0GATK4).'' LOCATION:Craik-Marshall Building SUMMARY:Variant Discovery with GATK4 URL;VALUE=URI:http://training.csx.cam.ac.uk/bioinformatics/event/2858057 END:VEVENT END:VCALENDAR