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Introduction to Variant analysis

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AvatarBérénice Batut AvatarYvan Le Bras
last_modification Last modification: Jul 9, 2021

What is Exome sequencing?


Exome sequencing

= Whole exome sequencing (WES or WXS)

Sequencing of all expressed protein-coding genes in a genome


Exome in Humans


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


Limits

Exome sequencing can not identify genetic variation in


2 tutorials for training on exome sequencing data analysis


Same goal

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


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.


### 2 tutorials


Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! Galaxy Training Network This material is licensed under the Creative Commons Attribution 4.0 International License.