3.3. Navigating VarSeq¶
VarSeq has several different types of views that can be arranged in numerous configurations. 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¶
3.3.1. 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 VSReport View
Table: For more information see Table View
VSClinical: For more information see VSClinical
Web Browser: For more information see Web Browser
3.3.3. 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 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 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 options 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…: 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.
3.3.4. 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.