====== 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 the Integrative Variant Analysis (IVA) tool is taught by members of the Clinical Bioinformatics Area with the aim of showing the latest advances in the prioritization and detection of disease variants * [[day1|Day 1: Introduction to Genomics, GATK Best Practices and Pipelining (Lee Lichtenstein, Tiffany Miller, Mark Walker, Andrea Haessly)]] * [[day2|Day 2:​ Germline short variant discovery (SNPs + Indels) (Lee Lichtenstein, Tiffany Miller, Mark Walker, Andrea Haessly)]] * [[day3|Day 3:​ Somatic variant discovery (SNVs + Indels + CNVs) (Lee Lichtenstein, Tiffany Miller, Mark Walker, Andrea Haessly)]] * [[day4|Day 4:​ Writing pipelines with WDL and running them in FireCloud (Lee Lichtenstein, Tiffany Miller, Mark Walker, Andrea Haessly)]] * [[day5|Day 5: Disease variant prioritization (Joaquín Dopazo, Javier Pérez-Florido, María Peña-Chilet)]]