Navigating VarSeq

VarSeq has several different types of views that can be arranged in numerous configurations. One possible configuration is displayed in oneVarSeqLayout. Each view will be discussed in detail.

Note

Each tab can be ripped out of the current view 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.

An example of a VarSeq layout

VarSeq Views

The VarSeq views 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 Report View
• Table: For more information see Table View
• VSClinical: For more information see VSClinical
• Web Browser: For more information see Web Browser
• Evernote: For more information see Evernote: Cloud-based Project Documentation

VarSeq Menus

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

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 Saving a Project as a Template 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 Source Wizard for more information.
  • Computed Data...: Choose from a list of algorithms to create a new field based on existing data in the table. See VarSeq Algorithms for more information.
• Export: This option gives the option to export data to multiple formats. See exportingData for more information.
• Evernote: Integrate VarSeq with Evernote using the options in this menu. See Evernote: Cloud-based Project Documentation for more information.
• 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 Data Source Library 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 Client-Side Integration.
• 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
  • Program Folder
  • Annotations Folder
• Proxy Settings...: Adjust proxy settings using this tool. See Adjusting Proxy Settings for more information.
• Options...: Change the default directories for the following folders:
  • Annotations Folder
  • Cached Files Folder
  • Database Folder
  • AppData Folder

Help Menu

The help menu contains the following:

• VarSeq Manual: Access to the embedded help manual
• VarSeq PDF Manual: A PDF version of the manual for easy printing.
• 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.

VarSeq Tool Bar

VarSeq tracks a primary view. On the primary view only there will be a global toolbar where there are a few icons that provide project level actions. These include:

• Import Variants: If variant data files have not already been imported into the project this icon will be active and allow you to import data into the 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.

  • 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 Source Wizard for more information.
  • Computed Data...: Choose from a list of algorithms to create a new field based on existing data in the table. See VarSeq 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 exportingData 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 options exports the data into the Convert Wizard so an annotation source can be created from the data. See Annotation Convert Source Wizard for more information.
  • XLSX File...: Export 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 in GenomeBrowse Menu: Data from the table can be visualized in GenomeBrowse, the options include, plotting BAM files , 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 BAM File for Current Sample: Plots the BAM file’s coverage and pileup data for the current sample if BAM files were linked to one or more samples on import.

    For Family data additional BAM plot options include:

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

    For Tumor/Normal Paired data additional plot options include:

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

  • 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.

• Save: Save the state of the project

• Close Project: Close the project

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

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

  • Annotations Folder
  • Cached Files Folder
  • Database Folder
  • AppData Folder

• Help: Access the VarSeq manual.

All other non-primary views will just contain the views and the specific view toolbars.

Closing non-primary view windows will just close that view or group of views. Closing the primary view will prompt for the save action and close both the project and VarSeq.

Saving a Project as a Template

To save a project as a template to be reused in the future with new data, go to File > Save Project as Template. To change the path for the folder to contain the template click on Browse. To reset the template folder to the default location click Reset.

Set the name of the template in the Name box, choosing a unique and identifiable name.

Fields are available to capture information about the template and this information will be displayed in the Create New Project window when the template is selected. Fill out as much information as you would like. Full font controls are available by right clicking in any of these text fields.

Note

To Tab within a text box:

• On Mac OSX use <Option> + <Shift> + <Tab>
• All other operating systems use <Ctrl> + <Tab>

If the template will require a specific genome assembly, make sure to leave the Specific Assembly box checked.

Save Project as Template by specifying a file and filling out the template information

In order to protect the filter chain and prevent modification, a lock is available to the left of the filter chain name. If it is locked, when you save a project as a template, there is the option to protect the filter chain lock. Any project created from a template with a protected filter chain will have a locked filter chain that cannot be unlocked.

Save Project as Template with the filter chain lock protected (locked)

When all of the information is provided, click Save. Now a new project can be created rerunning all annotation algorithms, filters, and creating all views with the same or with new data.

View Menus

Each view has a menu which can be accessed by right-clicking on the view tab. The view menu contains the following:

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

• 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.