NGS - Genome variant analysis

Date 8 - 9 December 2020
Speaker(s) Geert van Geest
ECTS 0.5
Fees *academic: 120 CHF   -   for-profit: 600 CHF
Cancellation deadline 24 Nov 2020
City Bern
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.

This course will take place in Bern with rules complying to the COVID-19 situation (distance and hygiene). In the event of new restrictions from the Swiss Government preventing us from organizing the course face to face, it will not be cancelled but switched to a virtual event (only for the registered participants) on the same date.

Please check that you are not coming from states and areas with an increased risk of infection as applications from these countries will not be accepted for courses held in classrooms.

Overview

The detection of genetic variation is of major interest in various disciplines spanning from ecology and evolution research to inherited disease discovery and precision oncology. Next generation sequencing (NGS) methods are very powerful for the detection of genomic variants. Thanks to its throughput and cost-efficiency it enables the detection of a large number of variants in a large number of samples. In this two-day course we will cover the steps from read alignment to variant calling and annotation. We will mainly focus on the detection of germline mutations by following the GATK best practices.

Audience

This course is intended for life scientists who are already familiar with general concepts of NGS technologies.

Learning objectives

At the end of the course participants should be able to:

  • Validate mapping output files
  • Perform local realignment to reduce false discovery
  • Aligne quality control
  • Call variants based on GATK best practices
  • Annotate Variants

Prerequisites

Knowledge / competencies:

Participants should have knowledge in NGS techniques, quality control and alignment to a reference genome. Participants should have a basic understanding of working with command line tools on UNIX-based systems. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module.

Technical:

Participants should bring their own computers and chargers (and adapters when coming from abroad).

Application

The registration fees are 120 CHF for academics and 600 CHF for companies.

Deadline for registration and free-of-charge cancellation is set to November 24. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available here.

You will be informed by email of your registration confirmation.

Location

Universität Bern, Hochschulstrasse 4 (main building of the University of Bern).

Schedule

Day 1 - 9h15 to 17h

Morning

  • Introduction to Variant discovery
  • Fetching sequencing data using Eutilities and SRA tools
  • Indexing references & mapping/sorting/indexing alignment

Afternoon

  • Differences in workflows between DNA-seq (WGS, WES) and RNA-seq
  • Marking duplicates
  • Realignment around SNPs and indels

Day 2 - 9h15 to 17h

Morning

  • Base quality score recalibration
  • Calling the variants (single and multiple samples)
  • Joint genotyping

Afternoon

  • Variant filtering
  • Variant annotation
  • Installing used software for a local use
  • Optional exam

Additional information

The course will be taught by Geert van Geest.

Coordination: Patricia Palagi

We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the session). 

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.

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