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
Calling variants in non-diploid systems
prokaryote
tutorial zenodo_link interactive_tour
Exome sequencing data analysis for diagnosing a genetic disease
tutorial zenodo_link workflow
Identification of somatic and germline variants from tumor and normal sample pairs
tutorial zenodo_link
Mapping and molecular identification of phenotype-causing mutations
tutorial zenodo_link workflow interactive_tour
Microbial Variant Calling
prokaryote
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.

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, Nick StolerNick Stoler, Wolfgang MaierWolfgang Maier, Torsten HouwaartTorsten Houwaart, Anika ErxlebenAnika Erxleben, Björn GrüningBjörn Grüning, Anna SymeAnna Syme, Simon GladmanSimon Gladman, Torsten SeemannTorsten Seemann

References