http://courseswiki.clinbioinfosspa.es/ 2026-04-25T02:13:22+00:00 http://courseswiki.clinbioinfosspa.es/ http://courseswiki.clinbioinfosspa.es/lib/tpl/bootstrap3/images/favicon.ico text/html 2018-09-13T04:37:41+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/day1?rev=1536813461&do=diff Day 1 (September, 17th): Introduction to Genomic Analysis Morning (10:15 – 13:45) 10:15 Registration and Welcome 10:45 Opening remarks 11:00 Introduction to Sequence data / pre-processing workflow 11:30 Introduction to Germline variant discovery Best Practices workflows 12:00 Coffee/tea break 12:30 Introduction to Somatic variant discovery Best Practices workflows 13:00 Introduction to pipelining with WDL + Cromwell + FireCloud 13:30 Closing question time text/html 2018-09-13T04:38:03+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/day2?rev=1536813483&do=diff Day 2 (September, 18th): Germline short variant discovery Morning (10:45 – 14:00) 10:45 Recap of germline variant discovery Best Practices 11:00 HaplotypeCaller 11:30 Joint-calling with GenomicsDB + GenotypeGVCFs 12:00 Coffee/tea break 12:30 Hands-on joint-calling text/html 2018-09-13T04:38:19+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/day3?rev=1536813499&do=diff Day 3 (September, 19th): Somatic variant discovery Morning (10:45 – 13:45) 10:45 Recap of somatic variant discovery Best Practices 11:00 Somatic SNVs and indels with Mutect2 11:45 Coffee/tea break 12:15 Hands-on Mutect2 Lunch Time (14:00 – 15:00) text/html 2018-09-13T04:38:32+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/day4?rev=1536813512&do=diff Day 4 (September, 20th): Pipelining Morning (10:45 – 13:45) 10:45 Recap of WDL/Cromwell basics 11:00 Hands-on WDL/Cromwell basics 12:00 Coffee/tea break 12:30 Self-paced WDL exercises Lunch Time (14:00 – 15:00) Afternoon (15:15 – 18:15) text/html 2019-10-21T10:48:55+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/day5?rev=1571654935&do=diff Day 5 (September, 21st): Disease variant prioritization Morning (10:00 – 13:30) 10:00 Introduction to openCGA and IVA for variant prioritization. 11:00 Coffee/tea break 11:30 Self-paced variant prioritization with IVA 13:15 Wrap-up and course closing text/html 2018-04-24T13:01:21+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/goals_of_the_hands-on_exercises?rev=1524574881&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 exercises 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 2018-09-13T10:08:23+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/prework?rev=1536833303&do=diff Previous requirements Software instructions In order to prepare your laptop in advance, there is a quick guide in the Broad's Institute Website. Furthermore, for the last day, it is strongly recommended to download the latest version of Google Chrome from text/html 2018-07-31T13:51:30+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/program_outline?rev=1533045090&do=diff Program outline The GATK workshop is a 4-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/FireCloud. 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. After GATK workshop, a tutorial on… text/html 2019-10-21T10:50:02+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/sidebar?rev=1571655002&do=diff * Start ---------- * Program: * Program outline * Goals of the hands-on exercises * Target audience ---------- * Detailed agenda: * Day 1: Introduction to Genomic Analysis * Day 2: Germline short variant discovery * Day 3: Somatic variant discovery * Day 4: Pipelining * Day 5: Disease variant prioritization ---------- * Workshop information: * Venue * Pre-Workshop text/html 2018-07-31T14:00:38+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/start?rev=1533045638&do=diff From reads to disease variants (Sevilla, Spain). 5-day workshop GATK Workshop - September 17-20, 2018 Disease variant prioritization tutorial- September 21, 2018 <https://software.broadinstitute.org/gatk/> Massive sequencing is becoming mainstream in many fields of biomedicine, including the clinical practice. However, the management of sequencing raw data to transform them into valuable biological information on variants and its further interpretation is still a complex task that requ… text/html 2018-07-31T14:13:41+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/target_audience?rev=1533046421&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 2018-09-17T09:12:14+00:00 http://courseswiki.clinbioinfosspa.es/gatk2018/venue?rev=1537175534&do=diff Venue * Instituto Andaluz de la Administración Pública (Old Pavilion of Puerto Rico) * 1, Johannes Kepler street (corner with Hermanos D'Eluyar street) * 41092, Isla de la Cartuja, Seville How to get there: Public transport is the best way to get to the venue. Bus lines C1 or C2 cross Américo Vespucio street in opposite directions (Facultad de Comunicación is the nearest stop)