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CHAPTER 5. WHOLE GENOME SEQUENCING (WGS)
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Some workflows take the gender into account. When asked for it, provide the gender of the
child (the proband).
Figure 5.46: Specify the proband's gender.
7. Specify the Hapmap populations that should be used for filtering out variants found in
Hapmap for the father (figure 5.47).
This can be done using the drop-down list found in this wizard step. Please note that the
populations available from the drop-down list can be specified with the Data Management
( ) function found in the top right corner of the Workbench (see section 4.1.4).
Figure 5.47: Select the relevant Hapmap population(s).
8. Specify the Hapmap populations that should be used for filtering out variants found in
Hapmap for the mother.
9. Specify the Hapmap populations that should be used for filtering out variants found in
Hapmap from the de novo assembly.
10. Set up the parameters for the Fixed Ploidy Variant Detection tool for the affected child.
11. Set up the parameters for the Fixed Ploidy Variant Detection tool for the father.