http://courseswiki.clinbioinfosspa.es/ 2026-04-30T15:42:16+00:00 http://courseswiki.clinbioinfosspa.es/ http://courseswiki.clinbioinfosspa.es/lib/tpl/bootstrap3/images/favicon.ico text/html 2019-06-19T14:09:48+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/accommodation?rev=1560953388&do=diff Accommodation suggestions Hotels with a close tramway stop Hotel Occidental Granada **** * Calle Alhamar, 46s 18004 Granada (Tramway stop: Recogidas) * Tel: (+34) 958 290 303 * 10 minutes by car to CMAT. Hotel Andalucía Center **** * Avenida Fuente Nueva, s/n 18002 Granada (Tramway stop: Hípica) text/html 2019-10-10T20:46:50+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/day1?rev=1570740410&do=diff Day 1 - Introduction | Monday October 21, 2019 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-workshop survey. text/html 2019-07-02T11:46:53+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/day2?rev=1562068013&do=diff Day 2 Germline | Tuesday October 22, 2019 Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself. text/html 2019-07-02T11:39:16+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/day3?rev=1562067556&do=diff Day 3 Somatic | Wednesday October 23, 2019 Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity. text/html 2019-07-02T11:47:29+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/day4?rev=1562068049&do=diff Day 4 Pipelining | Thursday October 24, 2019 Over the last three days, you’ve learned a lot about different pipelines and tools that you can use in GATK. Today we will be learning all about how those pipelines are written in a language called WDL. In the afternoon we cover other useful topics to working on the cloud, including Docker and BigQuery. text/html 2019-10-25T06:04:17+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/day5?rev=1571983457&do=diff Day 5 Disease variant prioritization | friday October 25, 2019 Morning (10:00 – 13:30) * Introduction to openCGA and IVA for variant prioritization. * Coffee break * Self-paced variant prioritization with IVA * Wrap-up and course closing text/html 2019-06-19T13:27:29+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/goals_of_the_hands-on_exercises?rev=1560950849&do=diff Goals of the hands-on exercises The hands-on exercises are designed to teach participants concrete skills and enable them to use the tools in their own research. In the hands-on sessions focused on analysis, we walk participants through exercises that teach them how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to common use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interac… text/html 2019-10-24T11:14:02+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/postworkshop?rev=1571915642&do=diff Post-Workshop Course survey : INB/ELIXIR-ES Short Term Feedback Survey GATK team survey : Survey Monkey text/html 2019-10-10T21:00:10+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/prework?rev=1570741210&do=diff Previous requirements Workshop materials All workshop materials can be found at here. This will later be populated with slides and worksheets, but right now just contains the instructions and data bundle Software instructions In order to prepare your laptop in advance, there is a quick guide with installation instructions text/html 2019-10-11T10:53:58+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/program_outline?rev=1570791238&do=diff Program outline The GATK workshop is a 5-day course formula where talks and hands-on exercises are interleaved to provide a well-balanced learning experience for participants. It covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/Terra. This includes the logic of the major pipelines, file formats and fata transformations involved, and hands-on operation of the tools using goal-oriented exercises. text/html 2019-10-24T11:04:32+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/sidebar?rev=1571915072&do=diff * Start ---------- * Program: * Program outline * Goals of the hands-on exercises * Target audience ---------- * Detailed agenda: * Day 1: Introduction * Day 2: Germline * Day 3: Somatic variant discovery * Day 4: Pipelining * Day 5: Disease variant prioritization ---------- * Workshop information: * Venue and social events * Accommodation * Pre-Workshop * Post-Workshop text/html 2019-10-24T15:16:04+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/start?rev=1571930164&do=diff From reads to disease variants (Granada, Spain). 5-day workshop GATK Workshop - October 21-24, 2019 Disease variant prioritization tutorial- October 25, 2019 <https://software.broadinstitute.org/gatk/> Massive sequencing is becoming mainstream in many fields of biomedicine, including the clinical practice. text/html 2019-01-11T10:59:46+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/target_audience?rev=1547204386&do=diff Target audience The workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or 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. text/html 2019-10-17T12:03:05+00:00 http://courseswiki.clinbioinfosspa.es/gatk2019/venue?rev=1571313785&do=diff [CMAT] Venue and social events Venue * IAVANTE CMAT * CMAT (Complejo Multifuncional Avanzado de Simulación e Innovación Tecnológica). Averroes room * Health Sciences Technology Park (Parque Tecnológico de la Salud) * 21, Avenida de la Investigación, 18016 Granada