Variant Analysis
Registration
Date: 22-25 October
Time: 9.30am – 3.30pm each day
Venue
Online
Places
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
£361 – University of Edinburgh staff/students
£380 – Other university or registered charity staff/students
£397 – Industrial researchers
Information
Overview
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
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.
Instructor
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