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Introduction to Variant analysis

Updated: PURL: gxy.io/GTN:S00099

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Requirements

Before diving into this slide deck, 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

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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.

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2 tutorials

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Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Author(s)	Bérénice Batut Yvan Le Bras
Reviewers

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.

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Introduction to Variant analysis

Requirements

What is Exome sequencing?

Exome sequencing

Exome in Humans

Goal of exome sequencing

Limits

2 tutorials for training on exome sequencing data analysis

Same goal

Similar data analysis approach

2 tutorials

Related tutorials

Thank You!

Requirements

Help