Dato & tid: 29. januar 2019
Sted: Auditorium, ACM15, AAU CPH, A.C. Meyers Vænge 15, København
Arrangør: DCCC/NEXT Bioinformatik
Deltagerpris: Undervisningen er gratis. Kost og logi for egen regning
Kontaktperson: Lise Tordrup Elkjær, tlf. 97 66 38 69, mail: lit@rn.dk
Tilmeldingsfrist: 21. december 2018

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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.