NGS - Genome Variant Analysis

Please note that this course is oversubscribed. We are still accepting applications, but your name will be placed on a waiting list.

Overview

Among other genomic applications, Whole genome sequencing “WGS”, Whole Exome Sequencing “WES” and RNA sequencing are used for the detection of genomic variants. On a genomic scale, variations manifest in the form of Single Nucleotide variants “SNVs”, insertions and deletions “Indels”, copy number variants “CNVs” or chromosomal rearrangements and are generally detected by comparing the sequencing data to a reference. The detection of genetic changes using the later technologies has many applications:

• Build population or subpopulations profiles
• Detect of hereditary changes that can be beneficial in some cases yet deleterious in others eg. Medelian diseases
• Assign tumor mutation profile eg. Cancer cell lines
• Correlate gene mutations to expression profiles and activity
• Annotate evidence based de novo changes in genomes

This 2 days course targets biologists and computational biologists. We will mainly focus on the detection of germline mutations by following the GATK best practices; we will also make use of other tools especially for the annotation part.

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
• Gather input information from public databases
• Perform local realignment to reduce false discovery
• Map quality control
• Call variants based on GATK best practices
• Annotate Variants

Prerequisites

Knowledge / competencies:

Participants should have Knowledge in Next generation sequencing techniques, pre-mapping quality control, filtering and mapping to reference genome. Participants should have a basic understanding of working with command line tools on Linux or Windows-based operating 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.

Application

Please note that this course is oversubscribed. We are still accepting applications, but your name will be placed on a waiting list.

The registration fees for academics are 100 CHF. Participants from non-academic institutions should contact us before application.

Deadline for registration and free-of-charge cancellation is set to January 29. 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

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 Walid Gharib

Coordination: Walid Gharib and Patricia Palagi

We will recommend 0.5 ECTS credits for this course (given a passed exam - optional - 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.

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