To use the Variant Comparison tool to analyze family data
When you use the Variant Comparison tool and you have family data available, you have three options for comparing samples. You can:
• Manually specify the expected variant types.
• Specify the relationship and the phenotype for each sample, and then load an Inheritance template to automatically adjust the expected variant types.
• Specify the relationship and the phenotype for each sample, and then carry out compound heterozygous filtering and review the results of this filtering in the Compound Heterozygous report.
1. On the Comparisons menu, click Variant Comparison Tool.
The Variant Comparison Tool window opens.
2. To load the files that are to be analyzed, do one of the following:
• On the Variant Comparison Tool main menu, click File > Load Projects.
• On the Variant Comparison Tool toolbar, click the Load Projects icon 
.
. The Load Projects dialog box opens.
3. For each family data project file that is to be analyzed, click Load Project File to open a Load NextGENe Project File dialog box, and then browse to and select the file.
After you load the first family data project file, the Variant Comparison dialog box is refreshed with columns for Relationship, Phenotype, and Mutation Type.
4. For each sample file, select the relationship and the phenotype, and if applicable, the expected variant type.
5. Click Next.
The Variant Comparison dialog box is refreshed with the settings for specifying the types of variants that are to be displayed in the Variant Comparison Tool report.
6. Do one of the following:
• To show only those variants that meet the expected variant type that you specified for each of the sample files, select Mutation type settings.
• To show variants that meet a specific pattern, select an Inheritance template or Compound heterozygous.
Setting | Description |
|---|---|
Template | Each template defines a specific inheritance pattern. Select a template to automatically adjust the expected variant types for the sample files based on the relationships and phenotypes settings for the project. Note: You can select from a pre-configured list of templates, or you can create your own custom template. |
Compound heterozygous | Select this option to carry out compound heterozygous filtering. The filtering results are displayed in the Compound Heterozygous report, which shows all possible combinations of two heterozygous variants in a gene if the variants meet the relationship and phenotype settings for the project. For example, if a Mother is Unaffected and a Father is Unaffected, but a Son is Affected, then one heterozygous variant must come from each parent. |
• Select Gene association, and then enter the minimum number of projects in which the same gene must have a variant (regardless of variant type and/or location) to report the gene in the output.
7. Do one or both of the following in the Filter and Display Settings pane:
• To specify the information that is to be displayed for each variant, click Mutation Report Filter/Display Settings.
Because the Variant Comparison Tool report settings are identical to those used in the Sequence Alignment Mutation report, the Mutation Report Settings dialog box opens. See Sequence Alignment Project Mutation Report Settings.
• To specify the tracks that are to be used in the comparison, click Tracks Filter/Display settings to open the Query Tracks dialog box and select and/or import the appropriate tracks. You can also set the display and filter settings for the selected tracks at this point.
 | For detailed information about loading track data for previously run projects, see the Geneticist Assistant User’s Manual or Online Help |
8. Click OK on the Variant Comparison dialog box.
The Variant Comparison Tool report opens. Green indicates a negative variant. “N/A” is displayed for allele calls for negative variants unless Check Allele Counts for Negative Mutations was selected.
9. If you selected Compound heterozygous filtering, then on the toolbar, click the Show/Hide Compound Heterozygous icon 
to open the Compound Heterozygous report.
to open the Compound Heterozygous report. | | Click the Show/Hide Compound Heterozygous report icon again to hide the report. |