Date & time: January 29 - February 1 2019
Location: Auditorium, ACM15, AAU CPH, A.C. Meyers Vænge 15, Copenhagen
Organiser: DCCC/NEXT Bioinformatik
Participant fee: Free of charge
Contact person: Lise Tordrup Elkjær, phone: 97 66 38 69, mail: lit@rn.dk
Registration deadline: December 21 2018
Find more information about the workshop
The workshop focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. Participants will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of their dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint discovery of germline short variants in cohorts, somatic short variant discovery using Mutect2, and copy number variation discovery using GATK-CNV. We also exercise the use of pipelining tools to assemble and execute GATK workflows.