VarSeq 1.1.1 Release Notes

New Features

  • Add PhoRank algorithm to support phenotype gene ranking. See PhoRank for more information.
  • Added Variant Databases as a default location in the Data Source Library under Local Annotations if it exists.
  • Added the ability to connect to local databases through the Database View to make user notes and editable annotations against variants. See Database View for more information.
  • Added a project note editor to take and store rich text notes in a project. See Note View for more information.
  • Added a log view to provide a detailed description of the actions taken in a project. See Log View for more information.
  • Added an option to import data as “Cancer Samples” with default parameters optimized for this data.
  • Added an option to filter cards to support Segment filtering. See Filter View for full details.
  • Replaced Excel XLS export with Excel XLSX to accommodate more variants and columns.
  • GenomeBrowse Features:
    • Save As Image now includes the option for saving in SVG format.
    • Added support for managing Genome Assembly views , genome segment order and visibility can now be changed. See Managing Genome Assembly Views for further details.
  • Added an advanced option to the Convert Wizard that allows MNP variants to be split into allelic primitives. See Allelic Primitives for specifics on this option.
  • Added a full screen toggle switch (<F11>) to handle sharing of projects across platforms where one or more windows were made full screen on Mac. This switch now allows the full screen windows to be adjusted on Windows, Linux and RHEL.

Bugs Fixed

  • Allow arrays of missing strings to be classified as missing for filter chains.
  • Fixed the variant source name when created by merging files. The number of additional files was off by one.
  • Removed common prefix after matching variants to alternate alleles or individual genotypes.
  • Fixed some edge case issues that occurred when selecting the Allelic Primitives advanced option for import of variant data.
  • Fixed alternate allele frequency calculations for multi-allelic sites so the matching alternate allele depth is being used.
  • Fixed the <Tab> control in Rich Text Edit dialogs including Save Project as Template. <Tab> and modifiers now work as expected.
  • Updated help URLs on the Import Wizard to link to the import section of the manual.
  • Fixed URLs in algorithm selection documentation to correctly link to manual and external web browsers when appropriate.
  • For variants with non-standard Ref/Alt pairs the Annotate Transcript tool will annotate based only on position and the Sequence Ontology and Effect(Combined) entries will then be listed as Invalid since they can not be produced for these variants.
  • Fixed exporting to VCF format when no genotype field is included.
  • Fixed –project command line argument and double-clicking on VarSeq projects to open the project in VarSeq.
  • GenomeBrowse bugs fixed:
    • Plots now correctly maintain y-axis zoom levels when selecting Save As Image or when adjusting the x-axis position.
  • Data Source Library bugs fixed:
    • Fixed right-click Open Folder on location sub-folders in the location pane of the Data Source Library.
    • Fixed sorting of fields to be in numeric order for certain fields including the size of the sources.
    • Ensure that the download window opens on top of viewers when a download of an annotation source is initiated from a Data Source Library dialog.

Polishes

  • Made folder path in the New Project dialog a hyperlink to open a system file explorer at that location.
  • Updated Import Options:
    • Added an option for the multi-allelic split algorithm to treat family, individual, and cancer samples differently. See Importing Data for the description of the options.
    • Multi-allelic split option no longer stripping common prefixes when reference and alternate alleles are the same. Also keeping reference alternate pairs where alternate is not present in any sample genotypes and combining them in their own record.
    • Samples with the same name will now be merged into separate sample records by default.
    • Polished information about advanced options and added direct links to the manual for more information about advanced import algorithm options.
    • Have left align use the project genome assembly’s reference sequence by default. In the advanced options for the summary page an option is now available to specify the assembly to use for left aligning the data.
  • Made export dialogs consistently sized and added more informative message about available options.
  • Added the current sample name (when available) to the Table name and the current filter button, i.e. Filter Chain: NA19240.
  • Prevented the upper right corner stash button from blocking the add ‘+’ tab button.
  • Changed column menu item to be “Search this Column” instead of “Add Table Filter for this Column” to clarify usage of the tool. See Table View for full details. Additionally removed table filter search options from primary table of split table view as they are not applicable to these column types.
  • Updated ! operator type in Expression Editor to Unary. See Expression Editor for a description of this operator.
  • Added informative error messages when the source types selected are not appropriate for annotation.
  • Added informative error messages when the source requires additional computation such as a genomic index before the source can be used for annotation. The error message now provides the name of the source(s) that could not be used for annotation.
  • Added Delete Algorithm button to algorithm error messages to make it easier to delete and clean up column groups with errors.
  • Replaced Evernote connection status messages with more informative messages to indicate when Evernote needs to be connected or when a note is loaded.
  • Added Select All and De-select All keyboard support (<Ctrl> + A and <Ctrl> + <Shift> + A respectively) to all web views.
  • Added search pop-up and keyboard search support (<Ctrl> + F) for all web views.
  • Updated Count Allelesalgorithm:
    • Added Hemizygous calls to the Homozygous Variant counts output as this is how they are treated for annotation and filtering purposes.
    • Made Allele Counts output alternate allele matching, should now have one count provided per alternate allele.
  • Adjusted layout of Add Location dialog in the Data Source Library to prevent the dialog from being too small for its contents.
  • On Windows and Linux to prevent a tab from docking, press <Ctrl> before ripping the tab out of a window.
  • Changed column grouping names for Annotate Transcript functions to include name of source used to easily differentiate annotations from separate sources.
  • Add downloads to the top of the download list in the Downloads dialog.
  • Better handling of font scaling when projects are saved across platforms.
  • Updates to shipped templates:
    • Exome Trio Template now includes filter chains for X-Linked and Known Rare Pathogenic workflows.
    • Updated gene panel templates to use the most recent versions of COSMIC and ClinVar annotations available.


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