4.2. Navigating VarSeq

VarSeq has menus and tool bars with functions, for use at the Project and View level, which are described in detail in this section. In addition, VarSeq has several different types of data and annotation views that can be arranged in numerous configurations. Each view is discussed in detail in the Section 4.5 VarSeq Views.

An Example of a VarSeq Layout

4.2.1. VarSeq Views

The VarSeq views (aka Tabs) include:

• Assessment Catalog: For more information see Assessment Catalog View

• Filter: For more information see Filter View

• GenomeBrowse: For more information see GenomeBrowse View

• Log: For more information see Log View

• Note: For more information see Note View

• Report: For more information see VSReport View

• Table: For more information see Table View

• VSClinical: For more information see VSClinical

• Web Browser: For more information see Web Browser

A View can be closed by clicking the X to the right of the View name in the tab. The + next to the right most open tab will open a new a View. The drop down on the left side of the menu allow you to change the data displayed in the view.

Note

Each view can be ripped out of the current layout and given its own window. Each window can have multiple views, and tabs can be stacked in the same location, so the possibilities are endless.

On Windows and Linux, to prevent docking when ripping a tab out press <Ctrl> then rip the tab out.

4.2.2. VarSeq Menus

VarSeq has four menus that will appear in the primary window these include File, View, Tools and Help.

The VarSeq Main Menu Bar

File Menu

The file menu contains program and project specific functions including:

• Create New Project: Close the current project (if one is open) and create a new project.

• Open Project: Close the current project (if one is open) and open a different project.

• Open Example Project: Close the current project (if one is open) and open an Example project that is created by Golden Helix and shipped with VarSeq. Example projects can be viewed and explored when in viewer mode.

• Open Recent Project: Close the current project (if one is open) and open a recently used project.

• Save Project: Save the project

• Save Project As: Save the project to a different folder or directory.

• Save Project As Template: Save the project as a template to be reused at a later time with new data. See saveAsTemplate for more information.

• Close Project: Close the current project.

• Import: If data has not already been imported into a project this option will be available to import data. After data has been imported this option will be replaced with Add.

• Add: If data has already been imported into a project this menu will be available to add or compute algorithms on the imported variants.

  • Annotation…: Select an existing data source to add additional annotation information to the table. In addition, from the Select Data Source dialog a new annotation source can be created. See Annotation Convert Wizard for more information.

  • Secondary Tables: Select additional annotations for CNV and Breakends and import relevant data. See VSClinical AMP for more information.

  • Computed Data…: Choose from a list of algorithms to create a new field based on existing data in the table. See Variant Algorithms for more information.

• Export: This option gives the option to export data to multiple formats. See Exporting Data from VarSeq for more information.

• Evernote: Allows access to the online note taking platform Evernote.

• Launch Another |vsName| Instance: Launches a new VarSeq instance.

• Log out <user name>: Close the project and log out of the user account.

• Exit: Close the project and exit VarSeq.

View Menu

The view menu contains the following:

• Open: Add additional views to the primary window. These views can then be moved to the desired location or ripped out into their own window.

• Dock Window: Certain views have additional dock windows that can be hidden or shown. This menu provides controls to hide or show those dock windows.

• Toolbar: Hide or show toolbars for views that have their own toolbars through this menu.

• Lock: Toggles the “Lock” state on views. When locked, views can not be closed or moved.

Tools Menu

The tools menu contains the following:

• Manage Data Sources…: Access the |dsl| to download, convert, add watched folders for annotation data sources. See The Data Source Library.

• Manage VSWarehouse…: Manage the connection between VarSeq and VSWarehouse. This can be accessed when a project is open or not, but some features, such as uploading samples to the warehouse and utilizing annotation sources require an open project. See VSWarehouse.

• Manage Gene Panels…: Opens the Manage Gene List Dialog which allows you to define and edit custom virtual gene panels. These gene panels can then be used by the algorithms and filter chain in VarSeq as well as in VSClinical. See Manage Gene List Dialog for more information.

• Downloads: Access the download manager to see the status of active or recently downloaded files.

• Open Folder: This sub menu contains short cuts to open folders that are important to the VarSeq program including:

  • User Data Folder

  • Project Folder

  • VarSeq Install

  • Chain Files

  • Assembly Files

  • Report Template

  • Annotations Folder

  • Assessment Catalogs Folder

  • Reference Samples

• Proxy Settings…: Adjust proxy settings using this tool. See Adjusting Proxy Settings for more information.

• Print Setttings…: Change the paper size and margins when printing.

• Memory and CPU Settings…: Change the Read Cache, Render Cache and CPU Core Limit.

• Custom Folder Path: Set the default location for AppData folder to store Annotations and preferences used by VarSeq

• Options…: Change the default directories for the following folders:

  • AppData Folder

  • Annotations Folder

  • Cached Files Folder

  • Assessment Catalog Folder

  • CNV References Folder

• Manage Reference Samples…: Manage the reference samples for the CNV Calling Algorithm.

Help Menu

The help menu contains the following:

• VarSeq Manual: Access to the embedded help manual

• Release Notes: Access to the release notes.

• Edit User Profile: Change your email address, password, name or address through this dialog.

• Activate a VarSeq License Key: A VarSeq license key can be entered into this dialog to register and access the full power of VarSeq. If a new key is provided it can also be changed in this dialog.

• About VarSeq: VarSeq version, install information and credits.

4.2.3. VarSeq Tool Bar

VarSeq has a toolbar below the main menu bar that provides project level functions. These include:

The VarSeq Project Level Bar

• Save Project: Save the project.

• Close Project: Close the current project.

• Add Menu: Additional data sources can be used to annotate the variants or computation algorithms can be run on the data by selecting an option from this menu.

  • Variant Annotation…: Select an existing data source to add additional annotation information to the table. In addition, from the Select Data Source dialog a new annotation source can be created. See Annotation Convert Wizard for more information.

  • Secondary Tables: Select additional annotations for CNV and Breakends and import relevant data. See VSClinical AMP for more information.

  • Computed Data…: Choose from a list of algorithms to create a new field based on existing data in the table. See Variant Algorithms for more information.

• Export Menu: Clicking on the Export Menu icon will reveal table export options. Each option will open a dialog to select one or more tables to export the filtered list of variants to a file of the specified type. By default the list of visible fields will be selected for export, but the state of these fields can also be adjusted in the export dialog. See Exporting Data from VarSeq for more information.

  • Text File…: Export the data to a text file. The delimiter and sub-delimiter can be specified in the export dialog. Column headers and column group headers can also optionally be selected in the dialog. See Export to Text.

  • VCF File…: Export the data to a VCF file. See Export to VCF.

  • Annotation File…: This option exports the data into the Convert Wizard so an annotation source can be created from the data. See Annotation Convert Wizard for more information.

  • XLSX File…: Exports the data to an Excel XLSX file. XLSX files are limited to 1,048,576 rows and 16,384 columns. See Export to Excel (XLSX).

• Plot Menu: Data from the table can be visualized in the View, the options include, plotting Alignment files (BAM/CRAM), creating a variant map for the unfiltered set of variants or creating a plot for columns or fields. By default the plot will initialize to the location specified by the currently selected row.

  • Plot Alignment File for Current Sample: Plots the alignment file’s coverage and pileup data for the current sample if alignment files were linked to one or more samples on import. For Family data additional alignment plot options include:

    • Plot Alignment File for Current Mother: Plots the alignment file’s coverage and pileup data for the current sample’s mother if alignment files were linked to one or more samples.

    • Plot Alignment File for Current Father: Plots the alignment file’s coverage and pileup data for the current sample’s father if alignment files were linked to one or more samples.

    • Plot Alignment File for Current Normal: Plots the alignment file’s coverage and pileup data for the current paired normal sample if alignment files were linked to one or more samples.

  • Plot Variants for Current Sample: Creates a variant map plot for the unfiltered set of variants for current sample.

  • Plot Variants for All Samples: Creates a variant map plot for the unfiltered set of variants for all samples.

    For Family data additional variant plot options include:

    • Plot Variants for Current Mother: Creates a variant map plot for the unfiltered set of variants for current sample’s mother.

    • Plot Variants for Current Father: Creates a variant map plot for the unfiltered set of variants for current sample’s father.

    For Tumor/Normal Paired data additional plot options include:

    • Plot Variants for Current Normal: Creates a variant map plot for the unfiltered set of variants for the current sample’s paired normal sample.

  • Plot Field…: Select a field from the sources in the table to plot in GenomeBrowse. Only one field can be selected at a time.

  • Annotation…: Opens the Select Data Sources To Plot dialog where you can select an Annotation track to display in GenomeBrowse.

• Manage VSWarehouse: Manage the connection between VarSeq and VSWarehouse. This can be accessed wether a project is open or not, but some features, such as uploading samples to the warehouse and utilizing annotation sources require an open project. See VSWarehouse.

• Sample Selection: Switch samples by using the arrow keys or the drop down menu.

• Options: Change the default directories for the following folders:

  • AppData Folder

  • Annotations Folder

  • Cached Files Folder

  • Assessment Catalog Folder

  • CNV References Folder

• Help: Access the VarSeq manual.

On the far right of the Toolbar, the number of samples and the unfiltered number of variants in the project are displayed.

4.2.4. Table View Menu

Each View has a menu which can be accessed by right-clicking on the View’s tab.

The Table View Menu

This menu contains the following:

• Open: Add another view at the same position in the current window.

• Recently Closed Tabs: Show the last 9 closed tabs and allows you to reopen them.

• Toolbars: Hide or show the toolbars for the current view.

• ID: <Identifier>: Modify the identifier for the current view. A custom identifier changes the Tab name of certain views (such as the Table view). It is also used to reference specific views in the command line runner mode. See IDs Used in Table Exports.

  Note: Starter templates will already have custom identifiers set for the various table views.

• Close: Close the current view.

• Close Other Tabs: Close all views behind the current view (aka tab) in the same docked location in the VarSeq window.