To compare family data
If the samples for a run are from a family, then you can use the Family Comparison option to compare the samples based on the relationships and phenotypes for each sample. At a minimum, you must select two parent samples and one child sample. You can always select more than one child sample.
1. If you have not done so already, open the Run tab for the appropriate run.
2. In the Samples pane, CTRL-click to select the family data that you are comparing.
 | At a minimum, you must select two parent samples and one child sample. You can always select more than one child sample. |
3. Right-click any selected sample, and on the context menu that opens, click Family Comparison.
The Family Comparison dialog box opens. If a patient is associated with a selected sample, then patient Relationship (Father, Mother, or so on) is displayed on the Relationship dropdown list; otherwise, you must select the appropriate relationship for the patient. Likewise, if the phenotype was included with the patient information, then the phenotype is automatically displayed on the Phenotype dropdown list for the sample, where Affected indicates that the patient has the phenotype and Unaffected indicates that the patient does not have the phenotype. If the phenotype is not automatically displayed for a sample, then you must select the appropriate value.
4. Do any or all of the following:
• On the Phenotype dropdown list at the top of the dialog box, select a different phenotype.
• On the Inheritance pattern dropdown list, select the appropriate value for the family, and if applicable, based on the selected Inheritance pattern, select Compound heterozygous.
| | Select Compound heterozygous to carry out compound heterozygous filtering. The filtering results are displayed in the Family Data Comparison Results pane. the results show all possible combinations of two heterozygous variants in a gene if the variants meet the relationship and phenotype settings for the parent samples. For example, if both the Mother and Father are Unaffected but a Son is Affected, then one heterozygous variant in the affected son must come from each parent. |
| | After you select an Inheritance pattern, the zygosity for each sample is automatically adjusted based on the selected inheritance pattern and the relationship and phenotype for the sample. If you select an incorrect Inheritance pattern based on the relationships and phenotypes, then “Error” is displayed instead of a valid zygosity value. |
• Indicate which columns to show or hide in addition to the default columns that are displayed for the family data comparison results: AF (Allele Frequency), Cov (Coverage), and/or RB (Read Balance).
• To display all the variants in each sample filtered by a selected panel, select Filter variants by panel, and then on the Panels dropdown list, select the appropriate panel.
• To display all the variants in each sample filtered by a selected pathogenicity, select Filter variants by pathogenicity, and then on the Pathogenicities dropdown list, select the appropriate pathogenicity.
5. Click OK.
The family data comparison is carried out. The Family Comparison tab opens. The left side of the Family Comparison Results pane shows sample-specific information. The results are shown using standard pedigree symbols. If the patient that is associated with a sample is affected, then the pedigree symbol is shaded; otherwise, the symbol is not shaded. You can hover your cursor over a column header to view specific details for the selected sample. The right side of the tab shows variant detail information.
| | Comparison of family data can take 30 minutes or more depending on a variety of factors, including the number of the samples that are being compared and the number of variants for each sample. |