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

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Variant analysis
plain text
Calling variants in diploid systems
tutorial
Calling variants in non-diploid systems tutorial
Exome sequencing data analysis for diagnosing a genetic disease
tutorial
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis tutorial
Identification of somatic and germline variants from tumor and normal sample pairs
tutorial
M. tuberculosis Variant Analysis tutorial
  • Mapping and molecular identification of phenotype-causing mutations
    tutorial
    Microbial Variant Calling tutorial
    Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data tutorial
  • 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 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.

    Maintainers

    This material is maintained by:

    AvatarBérénice Batut AvatarWolfgang Maier AvatarBjörn Grüning AvatarAnton 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:

    AvatarBérénice Batut AvatarYvan Le Bras AvatarAnton Nekrutenko AvatarNicola Soranzo AvatarAlex Ostrovsky AvatarNick Stoler AvatarWolfgang Maier AvatarTorsten Houwaart AvatarAnika Erxleben AvatarBjörn Grüning AvatarMarius van den Beek AvatarDave Clements AvatarDaniel Blankenberg AvatarPeter van Heusden AvatarSimon Gladman AvatarThoba Lose AvatarAnna Syme AvatarTorsten Seemann AvatarJasper Ouwerkerk AvatarHelena Rasche AvatarSaskia Hiltemann

    References