Variant Analysis

Exome sequencing means that all protein-coding genes in a genome are sequenced

Requirements

Before diving into this topic, we recommend you to have a look at:

Introduction to Galaxy Analyses
Sequence analysis
- Quality Control: slides slides - tutorial hands-on
- Mapping: slides slides - tutorial hands-on

Material

Lesson	Slides	Hands-on	Input dataset	Workflows	Galaxy tour
Introduction to Variant analysis	slides
Calling variants in diploid systems		tutorial Toggle Dropdown FR JA ES PT AR	zenodo_link	workflow
Calling variants in non-diploid systems prokaryote		tutorial Toggle Dropdown FR JA ES PT AR	zenodo_link		interactive_tour
Exome sequencing data analysis		tutorial Toggle Dropdown FR JA ES PT AR	zenodo_link	workflow
Identification of somatic and germline variants from tumor and normal sample pairs		tutorial Toggle Dropdown FR JA ES PT AR	zenodo_link
Mapping and molecular identification of phenotype-causing mutations		tutorial Toggle Dropdown FR JA ES PT AR	zenodo_link	workflow	interactive_tour
Microbial Variant Calling prokaryote		tutorial Toggle Dropdown FR JA ES PT AR	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 Batut,

Torsten Houwaart,

Björn Grüning,

Anton 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:

Torsten Seemann

References

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