NextGENe Online Help : NextGENe Viewer Comparison Reports and Tools : The Variant Comparison tool : To use the Variant Comparison Tool Top List function : To use the Top List function
To use the Top List function
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. Do one of the following:
• For a mutant sample/normal sample comparison, click Load Project File to open a Load NextGENe Project File dialog box, and then browse to and select the mutant project file, and then browse to and select the normal sample file.
 
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For a mutant/normal sample comparison, you must load the mutant sample file first, and the normal sample file second.
For either comparison type, 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. Do the following.
• Select Show shared/different and then:
• If you are carrying out a multiple sample comparison, select Show shared to show only those variants that are shared among all loaded projects.
• If you are carrying out a tumor sample/normal sample comparison, Select Show different to show only those variants that are present in only one of the projects.
• Set a Minimum coverage and Percent change to filter out variants if one sample fails the coverage setting or if the difference in allele frequency is less than the specified threshold.
 
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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.
 
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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.
8. Click the Top List icon.
The variants are ranked and sorted accordingly.
• For a mutant/normal comparison project, two additional columns (Category and Change) are displayed in the report, where Category indicates the variant type (1 = Gain of Heterozygosity, -1 = Loss of Heterozygosity, and 0 = Absolute Change), and Change indicates the absolute change in allele frequency between the two samples.
• For a multiple sample comparison project, one additional column, Similar, is displayed in the report, where similar indicates the similarity in allele frequency among all the different samples.