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CHAPTER 6. WHOLE EXOME SEQUENCING (WES)
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• Target Region Coverage Report One for each family member. The report consists of a
number of tables and graphs that in different ways provide information about the mapped
reads from each sample.
• Target Region Coverage One track for each individual. When opened in table format, it is
possible to see a range of different information about the targeted regions, such as target
region length, read count, and base count.
• An Amino Acid Track Shows the consequences of the variants at the amino acid level in
the context of the original amino acid sequence. A variant introducing a stop mutation is
illustrated with a red amino acid.
• Genome Browser View This is a collection of tracks shown together in a view that makes
it easy to compare information from the individual tracks, such as compare the identified
variants with the read mappings and information from databases.
6.3.4
Identify Rare Disease Causing Mutations in Family of Four (WES)
You can use the Identify Rare Disease Causing Mutations in a Family of Four (WES) ready-to-use
workflow to identifie de novo and compound heterozygous variants from an extended family of
four, where the fourth individual is not affected.
The Identify Rare Disease Causing Mutations in a Family of Four (WES) ready-to-use workflow
accepts sequencing reads as input.
How to run the Identify Rare Disease Causing Mutations in a Family of Four (WES) workflow
This section recapitulates the steps you need to take to start the workflow, each item corresponding to a different wizard windows. For more information on the specific tools used in this
workflow, see section 3.3.
To run the Identify Rare Disease Causing Mutations in a Family of Four (WES) workflow, go to:
Toolbox | Ready-to-Use Workflows | Whole Exome Sequencing ( ) | Hereditary
Disease ( ) | Identify Rare Disease Causing Mutations in a Family of Four (WGS
( )
1. Double-click on the Identify Rare Disease Causing Mutations in a Family of Four (WES)
tool to start the analysis. If you are connected to a server, you will first be asked where you
would like to run the analysis.
2. Select the targeted region file (figure 6.65).
The targeted region file is a file that specifies which regions have been sequenced, when
working with whole exome sequencing or targeted amplicon sequencing data. This file is
something that you must provide yourself, as this file depends on the technology used
for sequencing. You can obtain the targeted regions file from the vendor of your targeted
sequencing reagents.
3. Select the sequencing reads from the unaffected sibling (figure 6.66).
The sequencing reads from the different family members are specified one at a time in the
appropriate window. The panel in the left side of the wizard shows the kind of input that