Variant Analysis

2- 5 October 2023


Closed, Rescheduled


9.30am - 3.30pm each day




24 for each workshop

You will be contacted by our finance team for full payment. Once payment is made, your place will be confirmed and full details sent by our training team.

Registration fee

£380 - University of Edinburgh staff/students
£405 - Other university or registered charity staff/students
£430 - Industrial researchers


Contact our training team



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.

Who this course is for

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.



Frances Turner – Bioinformatician and Analyst, Edinburgh Genomics

Heleen De Weerd - Bioinformatician and Analyst, Edinburgh Genomics

Workshop format

The workshop consists of presentations and hands-on tutorials.


Topics covered

By the end of the course students will have covered:

  • Introduction to short read data

  • Whole genome sequencing (WGS) data QC

  • Data preprocessing

  • Short variant discovery

  • Germline joint variant calling

  • Genotype refinement

  • Variant filtering and evaluation

  • Variant annotation and interpretation

  • Somatic short variant discovery