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Compare variants across samples

The sections below describe how to create and modify a version of the Variants view that is optimized to compare all (or multiple) samples in the active GenVision Pro session. This view lets you compare variants from any combination of BAM, VCF, or .assembly experiments in the Experiments section of the Explorer panel or for sets created from those variants, which are located in the Variant Sets section.

Though we refer to this version as the “multi-sample Variants view,” it also supports single-sample analysis. Another version of the view supports only one sample and is described in the topic Analyze variants in a single sample. To learn how to tell one type of view from another, see the disambiguation table in Explore Variants and Structural Variations.


Create a new Variants view

Task How To
Create a table of unfiltered variants for all samples in the session Make sure at least two samples have been added to the project. Any selection made in the Experiments section will be ignored. Then do either of the following (only one of these options may be enabled):

  • Click the “Prepare Variants for Comparison” button in the otherwise empty Variants view.



    Note that each time an additional sample is added to the session, the Prepare Variants for Comparison button will appear. Click the button again to create a new table that includes the added sample(s).

  • Use Variants > Show Table > All Variants. While the view is being generated, the Variants view opens and you may see a progress bar and the Prepare Variants for Comparison button, which you can ignore. Note that if you later apply filters to the multi-sample table or create Variants views for a subset of samples in the session, you can use this command to open the unfiltered table showing all variants for all samples.

  • Use View > Variants > Variants > Show. If you have created a single-sample view, but have not yet created a multi-sample view, the Variants view will open but will display the button Prepare Variants for Comparison, which you will need to click to create the multi-sample view.
Create a table of filtered variants for all samples in the session Make sure at least two samples have been added to the project. Then use Variants > Show Table > With Filter. The Filter Variants wizard launches automatically at the Experiment screen. Once you click the Apply or OK button on this or any of the other wizard screens, the Variants view is generated or updated based on the filtering parameters you specified in the wizard. If you add more assemblies to the current session, their variants will automatically be filtered and added to the table.
Create a table of filtered variants for selected samples only First, use click, Ctrl/Cmd+click or Shift+click to select one or more rows in the Experiments section of the Explorer panel. Then use Variants > Show Table > With Filter for ‘n’ Selected Experiments. The Filter Variants wizard launches automatically at the Experiment screen. Once you click the Apply or OK button on this or any of the other wizard screens, the Variants view is generated or updated based on the filtering parameters you specified in the wizard. If you add more assemblies to the current session, their variants will not be added to the table.


Filtering which variants should be included in the view & saving filters for later use:

Task How To
Choose different filtering parameters for the active Variants view To return to the Filter Variants wizard and set up a different filter, use Variants > Filter > Filter or click on the Filter tool () and choose Filter.
Save the current filter settings to apply (manually) to future Variants views Use the menu command Variants > Filter > Save Filter or click on the Filter tool () and choose Save Filter.
Save the current filter settings to apply as the default for all future Variants views Use the menu command Variants > Filter > Save Filter as Default or click on the Filter tool () and choose Save Filter as Default.
Apply filter settings that were saved previously Use the menu command Variants > Filter > Apply Filter or click on the Filter tool () and choose Apply Filter.
Restore the DNASTAR default filter settings Use the menu command Variants > Filter > Restore DNASTAR Default Filter or click on the Filter tool () and choose Restore DNASTAR Default Filter.


Choose and rearrange table columns & saving these settings for later use:

Task How To
Choose and rearrange columns for the active Variants view Use Variants > Settings > Settings or click on the Choose or rearrange columns tool () and choose Settings to launch the Choose Columns dialog. For information on using this dialog and descriptions of available column types, see Choosing and understanding Variants view columns.
Group columns for the same sample together Variants > Settings > Group Columns by Experiment or click on the Choose or rearrange columns tool () and choose Group Columns by Experiment. This feature lets you view all values related to a particular sample in adjacent columns.

Group columns together based on variant type (e.g., “CDS”) Variants > Settings > Group Columns by Type or click on the Choose or rearrange columns tool () and choose Group Columns by Type.
Save the current column settings to apply (manually) to future Variants views Variants > Settings > Save Column Types or click on the Choose or rearrange columns tool () and choose Save Column Types.
Save the current column settings to apply as the default for all future Variants views Variants > Settings > Save Column Types as Default or click on the Choose or rearrange columns tool () and choose Save Column Types as Default.
Apply column settings that were saved previously Variants > Settings > Apply Column Types or click on the Choose or rearrange columns tool () and choose Apply Column Types.
Restore the DNASTAR default column settings Variants > Settings > Restore DNASTAR Default Column Types or click on the Choose or rearrange columns tool () and choose Restore DNASTAR Default Column Types.


Sort variants in the table:

Task How To
Sort variants in the active view according to a property Click any column header in the table to sort the entire table according to values in that column. Click the same header again to reverse the sorting direction.


Select variants in the table:

Task How To
Select all variants in the active Variants view Use Variants > Select > Select All.
Deselect all variants in the active Variants view Use Variants > Select > Select None.
Deselect the currently selected variants and instead select all other variants Use Variants > Select > Invert Selection.
Manually select variants Before making a selection, you may want to click once or twice on a relevant column header to sort the table in a way that facilitates selecting variants of interest to you. To make the selection, use Ctrl/Cmd+click or Shift+click to manually select rows in the table.


Miscellaneous tasks:

Task How To
Export data from the table Press the Export data tool () in the top right of the view. This opens a save dialog in which you can save the tabular data in comma-separated (.csv) or tab-separated (.tab) format. See Export data to a file for details.
Toggle between showing/hiding the table header Use the Show quick details tool () in the top right of the view.

Create a set of variants See Create and analyze variant sets to learn how to use the Create variant set tool ( ) and corresponding menu command.

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