To work with the Variant Comparison Tool report
After the Variant Comparison Tool report is generated, several other Variant Comparison tool functions become available from the report main menu.
• To view alignments for selected projects, click View > Check Projects to View Alignments, or on the report toolbar, click the Check Projects to View Alignments icon 
.
.The Sequence Display Settings dialog box opens. The dialog box displays all the projects for which you can view the alignments.
At a minimum, you must select the projects for which you want to view the alignments. You can also set any or all of the following options for the selected alignment projects:
Option | Description |
|---|---|
Base Display Size | Indicates the font size for the base display. You can leave this option set to the default value of 8, or edit as needed. |
Mark Center Lines | Selected by default. Indicates whether to show the center line (a green vertical line) in each alignment display. |
Show Translation | Select this option to add the Translation pane to the Variant Comparison Tool report. The pane displays the amino acid sequence in IUPAC nomenclature for each alignment display. |
Show Mutation Calls | Select this option to add the Mutation Calls pane to the Variant Comparison Tool report for each alignment display. Tick marks are displayed at the locations where mutation calls where made. |
After you set your options and click OK to close the Sequence Display Settings dialog box, a window that is linked to the report table for the selected projects opens. You can do the following in this window:
• Double-click a variant in the alignment view to change the focus of the report to the selected variant.
• Right-click a variant in the alignment view, and on the context menu that opens, select Go to position in Mutation report to change the focus of the report to the selected variant.
• Double-click a variant in the Mutation report to change the focus in the corresponding alignment view to the selected variant.
• To automatically save the Sequence Display Settings that you selected, click View > AutoSave Display Status. The next time you run a comparison in the Variant Comparison tool, these setting are automatically applied for the display.
• To copy a sequence in the Pile-up pane for an alignment project, press and hold the [Shift] key and the [Ctrl] key, and then click and hold the left mouse button and draw a box around the region of the sequence that you are copying. The selected region is filled with black. Right-click and select Copy Sequence or Copy As Picture to copy the sequence or image to your clipboard. Use standard keyboard commands or menu commands to paste the copied sequence or image into an application.
• To search the displayed alignment, click Search > Sequence Search, or on the report toolbar, click the Sequence Search icon 
. The Search dialog box opens, where you can indicate how you want to search the displayed alignment—by Sequence, by Position (chromosome, chromosome position (for example., 1, 20000)) or by Gene Name. You can also click Option to search by a reverse complement sequence.
. The Search dialog box opens, where you can indicate how you want to search the displayed alignment—by Sequence, by Position (chromosome, chromosome position (for example., 1, 20000)) or by Gene Name. You can also click Option to search by a reverse complement sequence.  | The Search Sequence function is enabled only when the Check Projects to View Alignments option is selected. |
• To change the current Mutation report display, click Settings > Settings to open the Mutation Report Settings dialog box. Select the Filter and Display options for the report.
| | For detailed information about the available settings on each of the tabs on the Mutation Report Settings dialog box, see Sequence Alignment Project Mutation Report Settings. |
• To change the current comparison settings, click Settings > Sample Settings to open the Load Project(s) dialog box, and then do any of the following:
• Select one or more projects for deletion.
• Add different projects for comparison.
• Modify settings for Relationship, Phenotype and/or Mutation Type for each project.
• Click Next, and then change the Comparison Type Settings.
• To select the tracks that are to be queried for the projects, click Settings > Tracks Settings > Query to open the Query Tracks dialog box.
| | For detailed information about loading track data for previously run projects, see the Geneticist Assistant User’s Manual or Online Help. |
• To change the display and filter settings for the tracks that are included with the projects, click Settings > Tracks Settings > Filter/Display to open the Variation Tracks Settings dialog box. Select the Filter and Display options for the report relative to the tracks.
| | For detailed information about the available settings on each of the tabs on the Variation Tracks Settings dialog box, see Variation Tracks Settings dialog box. |
• To save the report and/or related information in a variety of formats, click the indicated option on the File menu:
• Save Report - To save the report to a tab-delimited text (*.txt) file, or a VCF file.
The default Save as file type is tab-delimited text. To save in VCF format, select VCF file from the Save as type dropdown. A default name and location are provided for the file, but you can change both of these values.
| | You can also click the Save Report icon  on the report toolbar. |
• Save VarMD Report - To save the report as a VarMD report, which is a format that you can use in the third party VarMD tool.
• Save as Project Link - To save all the information for the currently displayed comparison (the samples, the comparison settings, and the report settings) in an .ini file. You must specify the file name. By default, the file link is saved in the project folder for the project that was loaded last for the comparison, but you can always select a different location.
• Load Project Link – To load a previously saved comparison, after you click this option, scroll to and select the appropriate project link. The comparison is loaded into the Variant Comparison tool. The comparison display is determined by the information (the samples, the comparison settings, and the report settings) that was saved for the project link.
• Save SNP Consensus – To save the consensus sequences for all the variants that are displayed in the Variant Comparison tool report. The sequences are saved to a .fasta file in the project output folder for the first loaded project. The default name for the file is based on the name of the first loaded project appended with _SNP_Sequences, but you can change one or both of these values.