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:
- Introduction to Galaxy Analyses
- slides Slides: Quality Control
- tutorial Hands-on: Quality Control
- slides Slides: Mapping
- tutorial Hands-on: Mapping
Material
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Introduction
Concepts of variant and genotype calling
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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Introduction to Variant analysis
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Calling variants in diploid systems
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Calling variants in non-diploid systems | |||||
Microbial Variant Calling |
Model Organisms
Variant calling for studying genomics of model organisms
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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Mapping and molecular identification of phenotype-causing mutations
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One Health
Variant calling for monitoring and preventing health threats
Human Genetics and Cancer
Variant calling pipelines for studying human genetic diseases and cancer
Data Management
Variant calling pipelines for interacting with human genetic databases
Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)
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Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons
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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.
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Editorial Board
This material is reviewed by our Editorial Board:
Bérénice Batut Wolfgang Maier Björn Grüning Anton NekrutenkoContributors
This material was contributed to by:
Peter van Heusden Thoba Lose Anna Syme Bérénice Batut Khaled Jum'ah Helena Rasche Simon Gladman Anika Erxleben Daniel Blankenberg Saskia Hiltemann David Salgado Dave Clements Wolfgang Maier Torsten Houwaart Nicola Soranzo Krzysztof Poterlowicz Tomas Klingström Yvan Le Bras Katarzyna Kamieniecka Björn Grüning Torsten Seemann Alex Ostrovsky Jasper Ouwerkerk Anton Nekrutenko Nick Stoler Marius van den BeekFunding
These individuals or organisations provided funding support for the development of this resource
References
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Umadevi Paila, Brad A. Chapman, Rory Kirchner, Aaron R. Quinlan: GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
GEMINI query is the most versatile of all the GEMINI tools. You can use it to ask questions in simple SQL -
Rasmus Nielsen, Joshua S. Paul, Anders Albrechtsen & Yun S. Song: Genotype and SNP calling from next-generation sequencing data
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. -
Erik Garrison and Gabor Marth: Haplotype-based variant detection from short-read sequencing
The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods, such as Bayesian statistical framework. -
Aaron R. Quinlan: Introduction to GEMINI
GEMINI query is the most versatile of all the GEMINI tools. You can use it to ask questions in simple SQL -
Torsten Seemann: Snippy: Rapid bacterial SNP calling and core genome alignments
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). -
Wolfgang Maier: MiModD Documentation
MiModD is a comprehensive software package for mapping-by-sequencing analyses -
Korbinian Schneeberger: Using next-generation sequencing to isolate mutant genes from forward genetic screens
Mapping the location of causal mutations using genetic crosses has traditionally been a complex procedure, but next-generation sequencing now allows the rapid identification of causal mutations even in complex genetic backgrounds