VarSeq 1.1.2 Release Notes

New Features

  • New Import Wizard features:
    • Now have the option to modify the field types from VCF files from site to sample and handle conflicts between site fields from multiple files.
    • Sample information can now be imported from a text file. Text files can include pedigree formatted data or a simple two column list of sample names and affection status. See Import Sample Information from Text File for more information.
  • New variant database features:
    • Added option to export an existing database schema to reapply to a new schema in the Manage Database dialog.
    • Added Project and Sample fields to automatically fill in the project and/or current sample when the variant was cataloged.
    • Added option to manually enter a variant without having to have that variant selected in a table.
  • Added outlier detection for Histograms which allows the user to filter outliers from the plot improving visualization of the data.
  • Count Alleles algorithm now accepts new sample level fields for grouping counts.
  • Export > Export to Text now includes the option to export column group names for the data. Each column group title is repeated so there is a corresponding value for each exported column.

Note: By default, the VCF Filter field is imported per-sample when merging VCF files. Because the previous behavior was to keep unique values across all samples, new projects may have more precise and stringent filtering based on this field.

Bugs Fixed

  • Fixed user credentials not being set after modifying a database, or accessing the database schema dialog.
  • Provide an algorithm out of date error for the CompoundHet filter card when disabling or enabling prerequisite filter cards.
  • No longer crashes when importing all unaffected samples into a template that requires at least one affected sample, such as a template with CompoundHet.
  • Fixed index assignment operator for arrays so Expression Editor can use specific entries to calculate new fields.
  • When exporting data using the Export to Text option the default extension is now set as *.txt if nothing is entered by the user.
  • Templates should now work if a field used to set up the template is present in the data but of a different type (i.e. sample vs site field).
  • Fixed the Annotate Transcriptalgorithm:
    • Exonic frameshifts are now classified as such even if they result in a downstream stop gain unless it results in the affected codon(s) to change to a stop gain.
    • A mutation which is 1 base exonic of a splice site is not called a splice_acceptor or donor.
    • Insertions bordering splice sites are annotated as either frameshift or splice_region.
  • Changed SSL (libssl.so.10 and libcrypto.so.10) bundled with RHEL build to prevent SSL Handshake errors when logging in.
  • Fixed Histogram reports to have intuitive buckets and clearer notation to indicate which values are being captured by the bucket for integer fields.

Polishes

  • Installing VarSeq will now clean up the install directory and remove files and libraries that are no longer used by the program.
  • Removed tab corner decorations e.g. (+) button unless there are tabs in the docking target area.
  • Ensure that a note is only created after it is opened and that changes are preserved when a tab is closed even if the project is not saved. Changes that are not saved are still discarded if the project is closed without saving changes.
  • Updates to Database views:
    • Modified the view to have vertical scroll bars for the top portion (fields in the database) and the bottom portion (recent assessments). This allows for resizing the variant database view.
    • Modified the view to line wrap the tool tips for fields to make them more readable.
  • Updates to the Data Source Library views:
    • When Data Source Library is launched from the Welcome Screen the available tracks are filtered down to show only those from the default human assembly. The assembly filter can be changed by selecting the new source from the drop down menu.
    • Rearranged annotation source columns in Data Source Library so when no assembly is selected the species and build information appears directly after the source name.
  • In the Import Wizard, the option to choose an assembly is now available in the Advanced Options for the final import algorithm selection page. The assembly file must match that used for alignment and the reference sequence has to be a local source in order to be used for the Left Align algorithm.
  • Now prompt user to download a local copy of the data source when the public copy is selected for annotation from the Data Source Library.
  • Updated default field list for dbNSFP annotation algorithm, the first column group is reserved for the prediction scores that contribute to the voting score only. All fields are available in the second column group.
  • Count Alleles output headers have been abbreviated to # Het and # HomoVar to reduce the width of the columns.
  • Adjusted spacing for the Excel XLSX export dialog window to remove extra spacing.


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