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
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

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 BatutAvatarWolfgang MaierAvatarBjörn GrüningAvatarAnton 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 BatutYvan Le BrasAnton NekrutenkoNicola SoranzoAlex OstrovskyWolfgang MaierTorsten HouwaartAnika ErxlebenBjörn GrüningMarius van den BeekDave ClementsDaniel BlankenbergPeter van HeusdenSimon GladmanThoba LoseAnna SymeTorsten Seemann

References