Introduction to Variant analysis

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# Introduction to Variant analysis

<div class="contributors-line">
		Authors: 
<a href="/training-material/hall-of-fame/bebatut/" class="contributor-badge contributor-bebatut"><img src="/training-material/assets/images/orcid.png" alt="orcid logo"/><img src="https://avatars.githubusercontent.com/bebatut?s=27" alt="Avatar">Bérénice Batut</a>

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<div class="footnote" style="bottom: 8em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: Jul 9, 2021</div>

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## Requirements

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

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)

- [Sequence analysis](/training-material/topics/sequence-analysis)
    - Quality Control: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html)
    - Mapping: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/mapping/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html)

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# What is Exome sequencing?

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### Exome sequencing

= Whole exome sequencing (WES or WXS)

Sequencing of all expressed protein-coding genes in a genome

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### Exome in Humans

- ~180,000 exons
- 1% of the human genome
- ~30 million base pairs

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### Goal of exome sequencing

Identify genetic variation that is responsible for both Mendelian
and common diseases without the high costs associated with
whole-genome sequencing

Exome sequencing is the most efficient way to identify the
genetic variants in all of an individual's genes

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### Limits

Exome sequencing can not identify genetic variation in

- All genes
- Mitochondrial genes
- “Structural variants”
- Triplet repeat disorders
- Other copy number variants
- Introns
- “Uniparental disomy”
- Control sequences
- Epigenetic changes
- Gene-gene (epistatic) interactions

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## 2 tutorials for training on exome sequencing data analysis

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### Same goal

Identify and annotate genetic variants in a family with two
parents and a child exome data

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### Similar data analysis approach

![Pipeline showing data preprocessing followed by variant calling with GATK/FreeBayes/Samtools/Naïve/VarScan going through filtering to a final VCF file. This is sent to GEMINI for ppost processing and variant analysis.](../images/genVAST.png)

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### 2 tutorials

- [Introductory tutorial](/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html)
- [Detailed tutorial](/training-material/topics/variant-analysis/tutorials/dip/tutorial.html)

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## Related tutorials

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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<a rel="license" href="https://creativecommons.org/licenses/by/4.0/">
This material is licensed under the Creative Commons Attribution 4.0 International License</a>.