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

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to Variant analysis
slides
Calling variants in diploid systems
tutorial zenodo_link workflow interactive_tour
Calling variants in non-diploid systems
tutorial zenodo_link workflow interactive_tour
Exome sequencing data analysis for diagnosing a genetic disease
tutorial zenodo_link workflow
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
tutorial zenodo_link workflow
Identification of somatic and germline variants from tumor and normal sample pairs
tutorial zenodo_link workflow
M. tuberculosis Variant Analysis
level level level
tutorial zenodo_link workflow
Mapping and molecular identification of phenotype-causing mutations
tutorial zenodo_link workflow interactive_tour
Microbial Variant Calling
tutorial zenodo_link workflow interactive_tour

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.

Maintainers

This material is maintained by:

Bérénice BatutBérénice Batut, Wolfgang MaierWolfgang Maier, Björn GrüningBjörn Grüning, Anton NekrutenkoAnton 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:

Bérénice BatutBérénice Batut, Yvan Le BrasYvan Le Bras, Anton NekrutenkoAnton Nekrutenko, Nicola SoranzoNicola Soranzo, Alex OstrovskyAlex Ostrovsky, Wolfgang MaierWolfgang Maier, Torsten HouwaartTorsten Houwaart, Anika ErxlebenAnika Erxleben, Björn GrüningBjörn Grüning, Marius van den BeekMarius van den Beek, Dave ClementsDave Clements, Daniel BlankenbergDaniel Blankenberg, Peter van HeusdenPeter van Heusden, Simon GladmanSimon Gladman, Thoba LoseThoba Lose, Anna SymeAnna Syme, Torsten SeemannTorsten Seemann

References