VarSeq 1.2.1 Release

New Features

  • Coverage statistics are now available in VarSeq. Coverage statistics are computed directly from BAM files for regions specified in a BED or other interval source. The statistics can either be viewed per variant, per region, or per sample. See Sample Coverage Statistics for more information.
    • BAM files can be linked to samples on import through the Import Wizard or through the import command for VSPipeline.
  • Moved the following toolbar items to the global toolbar for the main window:
    • Import/Add
    • Export tables
      • Exporting tables now allows for the explicit selection of a table to export. Multiple tables can still be exported simultaneously for XLSX export.
    • Plot data in GenomeBrowse
    • Current sample selection
  • Added controls for switching the type of a table, for example from a variant table to a variants by gene table or to a sample table.
  • Added a sample table containing sample fields specified on import. Any sample statistics that are computed are also added to this table, i.e. coverage statistics.
  • Now shipping a mini demo project with VarSeq that can be selected from the Recent Project list when VarSeq is initially installed in Viewer mode.

Bugs Fixed

  • Converted Annotate Transcript output for Sequence Ontology (Clinically Relevant) and Effect (Clinically Relevant) fields to categorical arrays to prevent algorithm error caused by too many unique strings for a categorical field.
  • Fixed issue with computations not finishing for filter cards created from string fields where the name of the field contained an operator string (ex. “in”).
  • Fixed Y-axis zoom in GenomeBrowse when not in automatic mode.
  • Name of sample in table column groups has been fixed to be the display name, i.e. Proband (NA12878) now instead of NA12878 when displaying all samples or only affected samples.
  • Fixed the broken revert link for Database Views to reset an assessment to a previous state.
  • Double-clicking on VarSeq project files (*.vsproject) to open the project directly in VarSeq is now working on Windows again.

Polishes

  • Filter Card layout updates:
    • Moved expression output number outside of the expression toggle layout.
    • Removed menu button on filter cards, the context menu is still available.
    • Added a toggle check box on all filter cards to enable/disable a filter card or container.
    • Removed filter card configure dialog box, instead the configure options are expandable by clicking on the wrench button.
    • Source/field selection is opened upon adding a filter
    • More informative auto titles (which now update as the filters change, not just on changing the configure options.)
    • All new filter cards are auto-titled by default/
    • Manual title can be set by double-click edit.
    • Return to auto title by double-click edit + click auto button.
  • Added the option to “Show All” or “Show Affected Only” to the bottom of the sample list in the current sample selection drop-down menu.
  • When data is imported as Tumor/Normal data, instead of “Show Affected Only” those options will be “Show Tumor Only”.
  • Changes to VarSeq Viewer Mode:
    • Menu items and actions are no longer hidden if they are not available in viewer mode. Instead, trying to select an action that is not available will open a dialog with the option to request a free trial or enter a license key. It should now be obvious why certain actions are restricted and that the software is in viewer mode.
  • Made segment filters more robust in handling spaces when getting segment names out of the text box.
  • Updated the file menu to have Add/Import/Export actions that match the updated main toolbar actions.
  • The Genotype algorithm has been moved from within the import function and will now appear as an optional algorithm that can be run. Genotypes can now be computed by going to Add > Computed Data… and selecting the Genotype algorithm under the Data Transformation options.
  • Removed restrictions on sample limits that can be viewed in the sample table in the Import Wizard.
    • Editing is now allowed when importing more than 100 samples.
    • If importing more than 1000 samples, double-click on cells to edit them.
  • Added filter card and filter container descriptions to the detailed report for the Detail View generated when clicking on a filter card or container.


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