Working with an Existing Project

How do I open an example or existing project?

  • To open an example project, select the project from the list of example projects, or go to File > Open> Example Project and select one of the examples.
  • To open an existing project, either click on Open Existing Project, or select the project from the list of recent projects.

How do I change the samples visible or how
the sample data is collated in a table?

  • To change the samples visible or how the sample data is collated in a table, click on the sample display options icon and adjust either the Collated By or the visibility option for the samples. See Figure 1.
Figure 1: Sample display options icon in VarSeq

  • If the samples were imported with family information or tumor/normal pairs you have the option of only showing the current sample and linked samples (Current and Parents or Tumor and Normal). Otherwise these option are not available.

How do I change which columns or fields are
visible in a table?

  • Click on the Hide/Show icon. Entire groups of columns fields can be hidden or shown by toggling the check boxes. See Figure 2.
Figure 2: The Hide/Show icon in VarSeq
  • Expand each group to select particular fields to hide or show.
  • Click on Select All or Unselect All either by a column group name or below all of the column groups to toggle the selection of more than one field at a time.

How do I sort data in a column?

  • To sort data in a column, right-click on the column header and select one of the sorting options.
  • To unsort the data, right-click on any column and select Sort in Genomic Order.

How can I visualize data in a particular filter?

  • Click on the number of variants on the Filter Card and the table view will show the results of that step in the filter chain.
  • To view the variants as they pass through each filter card, click on the Expand button on a particular card. The highlighted categories generally display the number of variants that pass the criteria specified by the card. Clicking on any of the numbers in the filter card will display those variants in the table view.
  • Right-click on any filter card and select either Results Up Through This Filter or Results For Only This Filter.

The difference between result display options
Results Up Through This Filter Selecting this option displays all variants that remain in
the Filter Chain after applying the current filter. This means the particular filter criteria and all previous filter criteria have been met for the variants displayed in the Table View.

Results For Only This Filter
Selecting this option displays all variants from the original set of variants that meet the filter criteria of only the current filter.

How do I change the sample in the project?

  • To quickly reprocess the filter chain for new samples, you can use the arrow keys on either side of the current sample menu to switch samples. See Figure 3.
  • To navigate through all samples in the project, click on the down arrow or right click in the current sample menu and select Show All then click on the right or left arrows or click on the down arrow and select a sample. See Figure 3.
  • To change the current sample, select the sample from the drop down menu. See Figure 3.
Figure 3: Arrow keys and dropdown menu to change samples

How do I hide or stash a view?

  • Click on any gray X in the corner of any tab. This will delete the view but it can be restored at any point with the existing settings. See Figure 4.
  • To stash a view, hover over one of the four corners of the window until the stash icon appears. Click on the icon and the tabbed view(s) closest to that corner will be stashed. See Figure 4.
Figure 4: Close a tab with the X in the corner or stash a view with the stash icon

How do I rearrange the layout of tabs?

  • Tabs (or views) can be rearranged like tabs in modern web browsers. Just click on a tab and drag and drop on an existing view to stack the tab, or hover over an edge of the window. If a placement hint appears, the tab can be dropped in that location.
  • You can take advantage of multiple monitors by ripping tabs out of the main window and creating new windows. Additional tabs or views can be added to the new windows as well.

How do I add a new view or tab?

  • Click on any plus sign next to a tab and select the type of tab to add to the stack of tabs at that current location.
  • To add a new tab to one of the four corners of a VarSeq window, right-click on a stash icon and select the type of tab to add.

How do I visualize data in GenomeBrowse?

  • To plot the variants, click on the plot button in the main tool bar and select Plot Variants.
  • Similarly data from any numeric column and Sample Alignments from BAM files (if linked on import) can be visualized in GenomeBrowse through the plot menu on the main tool bar.
Figure 5: Plot variants and BAM files for samples in the project

How do I share a VarSeq project with a
colleague?

  • Anyone who has installed VarSeq can view existing projects. Have your colleague install VarSeq, and send them the entire project folder.
  • They will be able to download any required annotation sources if they are publicly available.
  • Send with the project any proprietary annotation sources, or sources created locally.
  • VarSeq Viewer allows free access to view projects, explore the filter chain and export results. Limitations include:
    • New projects cannot be created
    • New annotations cannot be added
    • Existing projects cannot be saved
    • Databases cannot be created or modified
    • Many filter chain modifications are disabled

How do I take notes or save important
information about a project?

  • You can create a project note by adding a Note View and selecting Open a New Note.
  • Each project can contain multiple notes, to rename the note to have an informative name, replace the note header Untitled Note with a more informative name.
  • Images can be captured from an open GenomeBrowse view. Click on the camera icon within Genomebrowse to include a GenomeBrowse screenshot that includes all plots. Click on the camera icon to only insert a screenshot of the selected plots.
  • Regions in GenomeBrowse can be bookmarked by clicking on the bookmark icon. You can then jump to this region by clicking on the link.
  • Notes can be exported as either HTML or PDF by clicking on the export button.

Updated on January 22, 2021

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