Variant Analysis

Genetic differences (variants) between healthy and diseased tissue, between individuals of a population, or between strains of an organism can provide mechanistic insight into disease processes and the natural function of affected genes.

The tutorials in this section show how to detect evidence for genetic variants in next-generation sequencing data, a process termed variant calling.

Of equal importance, they also demonstrate how you can interpret, for a range of different organisms, the resulting sets of variants by predicting their molecular effects on genes and proteins, by annotating previously observed variants with published knowledge, and by trying to link phenotypes of the sequenced samples to their variant genotypes.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Introduction

Concepts of variant and genotype calling

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Variant analysis
Calling variants in diploid systems
Calling variants in non-diploid systems
Microbial Variant Calling

Model Organisms

Variant calling for studying genomics of model organisms

Lesson Slides Hands-on Recordings Input dataset Workflows
Mapping and molecular identification of phenotype-causing mutations

One Health

Variant calling for monitoring and preventing health threats

Lesson Slides Hands-on Recordings Input dataset Workflows
Avian influenza viral strain analysis from gene segment sequencing data
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
M. tuberculosis Variant Analysis
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
Pox virus genome analysis from tiled-amplicon sequencing data

Human Genetics and Cancer

Variant calling pipelines for studying human genetic diseases and cancer

Lesson Slides Hands-on Recordings Input dataset Workflows
Exome sequencing data analysis for diagnosing a genetic disease
Identification of somatic and germline variants from tumor and normal sample pairs
Somatic Variant Discovery from WES Data Using Control-FREEC
Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/variant-analysis-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBjörn Grüning avatar Björn GrüningAnton Nekrutenko avatar Anton Nekrutenko

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

orcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAnna Syme avatar Anna Symeorcid logoHelena Rasche avatar Helena Rascheorcid logoKatarzyna Kamieniecka avatar Katarzyna KamienieckaMarius van den Beek avatar Marius van den Beekorcid logoSimon Gladman avatar Simon Gladmanorcid logoYvan Le Bras avatar Yvan Le BrasTorsten Seemann avatar Torsten SeemannJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoKhaled Jum'ah avatar Khaled Jum'ahorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoBjörn Grüning avatar Björn Grüningorcid logoDave Clements avatar Dave ClementsThoba Lose avatar Thoba Loseorcid logoNicola Soranzo avatar Nicola SoranzoNick Stoler avatar Nick StolerAnton Nekrutenko avatar Anton NekrutenkoDavid Salgado avatar David Salgadoorcid logoWolfgang Maier avatar Wolfgang MaierTorsten Houwaart avatar Torsten Houwaartorcid logoTomas Klingström avatar Tomas Klingströmorcid logoBérénice Batut avatar Bérénice Batutorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowicz

Funding

These individuals or organisations provided funding support for the development of this resource

References