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.

Requirements

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

Material

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

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

Data Management

Variant calling pipelines for interacting with human genetic databases

Lesson Slides Hands-on Recordings Input dataset Workflows
Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)
Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons

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

Contributors

This material was contributed to by:

orcid logoPeter van Heusden avatar Peter van HeusdenThoba Lose avatar Thoba Loseorcid logoAnna Syme avatar Anna Symeorcid logoBérénice Batut avatar Bérénice Batutorcid logoKhaled Jum'ah avatar Khaled Jum'ahorcid logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoSaskia Hiltemann avatar Saskia HiltemannDavid Salgado avatar David Salgadoorcid logoDave Clements avatar Dave Clementsorcid logoWolfgang Maier avatar Wolfgang MaierTorsten Houwaart avatar Torsten Houwaartorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoKrzysztof Poterlowicz avatar Krzysztof Poterlowiczorcid logoTomas Klingström avatar Tomas Klingströmorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoKatarzyna Kamieniecka avatar Katarzyna Kamienieckaorcid logoBjörn Grüning avatar Björn GrüningTorsten Seemann avatar Torsten Seemannorcid logoAlex Ostrovsky avatar Alex OstrovskyJasper Ouwerkerk avatar Jasper OuwerkerkAnton Nekrutenko avatar Anton NekrutenkoNick Stoler avatar Nick StolerMarius van den Beek avatar Marius van den Beek

Funding

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

References