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.


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



Concepts of variant and genotype calling

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

Model Organisms

Variant calling for studying genomics of model organisms

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

    Variant calling pipelines for studying human genetic diseases and cancer

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    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 tutorial

    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

    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.


    This material is maintained by:

    orcid logoAvatarBérénice Batutorcid logoAvatarWolfgang Maierorcid logoAvatarBjörn GrüningAvatarAnton Nekrutenko

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


    This material was contributed to by:

    orcid logoAvatarAnna Symeorcid logoAvatarKrzysztof Poterlowiczorcid logoAvatarYvan Le Brasorcid logoAvatarSimon GladmanAvatarKatarzyna Muratorcid logoAvatarWolfgang MaierAvatarNick StolerAvatarJasper Ouwerkerkorcid logoAvatarNicola SoranzoAvatarThoba LoseAvatarKhaled Jum'ahorcid logoAvatarSaskia Hiltemannorcid logoAvatarDaniel BlankenbergAvatarAnton NekrutenkoAvatarAlex OstrovskyAvatarDavid Salgadoorcid logoAvatarAnika ErxlebenAvatarMarius van den Beekorcid logoAvatarDave Clementsorcid logoAvatarPeter van HeusdenAvatarTorsten HouwaartAvatarTorsten Seemannorcid logoAvatarHelena Rascheorcid logoAvatarBérénice Batutorcid logoAvatarBjörn Grüning