To use the Variant Comparison tool to compare multiple projects
You can load up to 20 project files when comparing multiple projects.
1. On the Comparisons menu, click Variant Comparison Tool.
The Variant Comparison Tool window opens.
2. To load the files that are to be compared, 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 Variant Comparison dialog box opens.
3. For every project file that is to be loaded into the tool, click Load Project File to open a Load NextGENe Project File dialog box in which you can browse to and select the project file.
After you load the first project file, the Variant Comparison dialog box is refreshed with columns for Relationship, Phenotype, and Mutation Type.
4. 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.
5. Specify the type of variants that are to be displayed in the Variant Comparison Tool report.
Setting | Description |
|---|---|
Comparison Type | |
• Show all | Show all variants in all projects. |
• Show shared/different | Select showed shared/showed different, and then select one of the following: |
• Show shared | • Show only those variants that are shared among all loaded projects. |
• Show different | • Show only those variants that are present in a single project when comparing only two projects or only those variants that are shared among some, but not all the projects, when comparing more than two projects. |
• Minimum coverage • Percentage change | • The minimum coverage threshold that is required in all samples for a variant to be included in the Variant Comparison Tool report. • The difference (in percentage) in the mutant allele frequency that is required for variants in two samples be categorized as “Different.” If two samples have the same variant that is found at frequencies with a difference that is less than the indicated threshold, then the variant is categorized as “Shared” for the samples. |
Exclude 0% variants | Available only if Show shared is selected. Ignore the Percentage Change threshold and always considers two samples as being different if a variant is called in one of the samples but it is not called in the other sample and the variant allele is found at 0% in the other sample. |
• Low coverage SNPs | View all variants in all projects that meet the indicated low coverage requirements. Note: If you select Low Coverage SNPs, then you can accept the default value of 10 for Display Low Coverage SNPs, or you can modify the value. |
Gene association | At least “x” number of projects have a variant in the same gene, regardless of variant type and/or location. |
 | You can select only one filtering option—Show All, Show shared/different, Low Coverage SNPs, Template, or Compound Heterozygous. |
6. 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. See Variation Tracks Settings dialog box.
• To query the variant tracks only for the mutation positions that are displayed based on your comparison settings and filter settings, select Quick Query (Displayed Mutations only).
| | For detailed information about loading track data for previously run projects, see the Geneticist Assistant User’s Manual or Online Help. |
7. 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.
8. Optionally, continue to To work with the Variant Comparison Tool report.