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What is the Whole Exome Sequencing (WES)?
What is the goal of it?
Applications of exome sequencing.
What is comprised?
Motivation and comparison to other approaches.

Exome sequencing is only able to identify those variants found in the coding region of genes, which affect protein function.

All the exons.All the translated genes.All the protein coding genes. Specific portion of the gene we believe is the most important (exons) where most mutations occur.

Extract the exons (segments). Sequence the segments

1- Break down the genome to exons and introns
2- Amplify the exons
4- to increase the number of genes and take it to higher amount, we need to use any amplification process.
3- Select the exons only. Called the amplification of target and that can be achieved by 4 different techniques. Microarray based hybridization, PCR, molecular inversion probe (MIP), and hybridized technology.
5- Sequence it with any kind of next generation sequencing. Like illumine
6- then we can find out if there is any disease, by different stages. culstring, read the data, aligned read, exons read

Now we are able to look at all 20,000 genes at one time by using powerful computers.

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https://www.broadinstitute.org/gatk/guide/bp_step.php?p=1

How to do whole exom analysis?
What are the steps?
Need different tool for each step. What they are?

Raw FASTQs to raw reads via mapping>bwamem tool
Raw reads to analysis-ready reads>picard tools
Local realignment around indels> Genome Analysis Tool Kit
Base quality score recalibration> Genome Analysis Tool Kit
HARD FILTERING> Genome Analysis Tool Kit

Write about each tool too.