Workshops and courses

ELIXIR node event Variant Analysis

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Date: 17 - 20 March 2025

This course aims to provide an introduction to the principles of short variant discovery (both germline and somatic) from short read data. We will look at a complete workflow, from data QC to functional interpretation of variant calls. The practical sessions will focus on running the GATK pipeline from the Broad institute. https://gatk.broadinstitute.org/hc/en-us

Keywords: GATK, Germline, Short read, Somatic, Variant

Prerequisites:

Attendees must have a working knowledge of how to use the Linux BASH command line; our 1-day 'Linux for bioinformatics' course is a suitable background.

Learning objectives:

  • Data preprocessing
  • Genotype refinement
  • Germline joint variant calling
  • Introduction to short read data
  • Short variant discovery
  • Somatic short variant discovery
  • Variant annotation and interpretation
  • Variant filtering and evaluation
  • Whole genome sequencing (WGS) data QC

Organizer: Edinburgh Genomics

Target audience: This course is intended for researchers who need to analyse genomic data in order to call genomic variants. Aside from a basic understanding of molecular biology, attendees must have a working knowledge of how to use the Linux BASH command line; our 1-day 'Linux for bioinformatics' course is a suitable background.

Event types:

  • Workshops and courses

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