VarSeq 1.1.4 Release Notes

New Features

  • Tumor/Normal Support: Added the ability to import tumor/normal pairs through the import wizard. See Select Relationship for more information.
  • Added a Tumor-Normal Template with a generic workflow to find variants present in the tumor samples not present in the matched normal samples.
  • PhoRank can now read phenotype mappings from a “Phenotype” sample entity field if sample information is loaded from a text file. This allows PhoRank to be included in templates.
  • Now able to import variants from text files provided by 23andMe. See Importing Data for further details.
  • Filtering and importing of variants located only in regions specified by an annotation file can now be performed on import. See Import Summary for more information.
  • Include helpful information on INS/DEL/SUB/MNP variants in the detail view for a variant report. The length and type of variant is now included after the Ref/Alt string in the title.
  • New pipeline commands were added to:
    • Accept the EULA from the command shell
    • Download required sources
    • Get a list of pending tasks
    • Wait for variant annotation to complete
    • Set an environment variable GOLDENHELIX_USERDATA on launch to specify the path of the VarSeq properties file “vsprops.json”.

Bugs Fixed

  • Pipeline bugs fixed:
    • If an invalid template name is specified when creating a project, do not create the project folder.
    • Batch command can now be run without a license
    • If an invalid file is used to specify sample fields, provide an informative error message instead of crashing
    • Fixed a bug which can cause successive exports to contain different columns
  • Convert Wizard bugs fixed:
    • Fixed error when a CSV file was selected for converting that caused the comma delimiter to be treated as part of the field data.
  • Import Wizard bugs fixed:
    • Fixed problem preventing importing variants from certain VCF files that resulted in the error “No data was provided to write the source”.
    • Do not compute Alt Allele Frequency when the frequency should be missing. This bug resulted in frequency values less than 0.
  • Fixed issue with missing View menu on MacOS.
  • Handle full screen mode on MacOS better.
  • Fixed issue with Lin64 version that caused VarSeq to shutdown when opening and closing the Select dialog in the filter card control dialog.
  • Fixed a crash that could occur if a filter card is moved during the evaluation of the filter chain
  • Fixed issue in VCF export when subfields were being exported when the field group option was not selected.
  • Prevent accidental deletion of filter expressions from within a filter card when pressing delete on the keyboard.
  • Fixed <SHIFT>+. and . keyboard shortcuts. Now . will display the filter chain output and <SHIFT>+. will display the filter chain input for all unlocked table views.
  • Algorithm crashes fixed:
    • Prevent crash when the reference length does not match the segment length and annotating by transcript.
    • Prevent Compound Het algorithm from crashing when no probands are present in data.
  • Fixed issue with identifying Compound Hets when a float array frequency field was selected.
  • Allow GenomeBrowse to plot data from a VCF file that contains string arrays instead of giving the error that mapFields cannot be converted from StringArray to String.
  • Ensure that the location needed by VarSeq for the properties file exists, if it doesn’t then the location is created on launch of the application.
  • Fixed issue with Data Source Library preventing downloading from the public repository a previously downloaded file that is no longer present in the user annotations folder.

Polishes

  • Import Wizard polishes:
    • Make it more obvious when an invalid segment is entered into the genomic regions input box and prevent importing until a valid segment is entered or the option is cleared.
    • Report any genomic region subset specified in the Import Wizard in the node change log.
    • Provided more informative errors when unable to sort VCF data on import.
    • Allow entity information to be imported from a text file regardless of the amount of samples.
    • Allow missing affection status when importing from an entity text file.
    • Trim white space from the sample field information after splitting on the specified delimiter.
    • Automatically set sample fields named either “Phenotype” or “HPO” (case-insensitive) to the optional Phenotype field that can be used for automatically filling in the PhoRank phenotype fields.
    • Remove quotes from string fields.
    • Handle string list fields when including the field in the sample information.
    • Prevent upgrading INFO level filter field to a sample matrix field if one already exists in the VCF file.
    • Added less strict matching for pedigree fields when importing family information from a text file.
    • Removed ‘END’ field from VCFs that are importing through the merge transform.
  • After import, if no data could be imported the error message is clarified to indicate it could be due to filters placed on the data during import.
  • Pipeline polishes:
    • Allow for help and shell commands to be parsed from the command line without needing to prefix with -c
    • Remove an empty set of temporary folders from the vspipeline working directory on Linux and RHEL after exporting to XLSX.
    • Allow shell commands to be quoted or unquoted when entered from the command line
    • Command result output now supports displaying duplicate key values
    • Import command now accepts parameters to subset by FILTER field or genomic region
    • vspipeline returns exit code 1 if any command fails during execution
    • Error messages have been made more specific during license verification
    • Warn user if sources need to be downloaded for template to complete, but still allow data to be exported
    • Output annotation progress
    • Use current working directory to resolve relative paths passed into commands
    • Add argument to import command to subset using a gene source
    • The parameter affected has been changed to affected_only to allow user to iterate over only affected samples or all samples
  • Convert Wizard polishes:
    • Added support for converting BED files with only chromosome, start position, and stop position.
    • Added support for vcf.gz (gzip) files to be run through the Convert Wizard.
  • Improved accuracy of progress tracking and time estimation for long running tasks.
  • Now only showing the appropriate labels for the available samples in the filter card configuration options.
  • Registering for VarSeq now has “Keep me informed!” unchecked by default and the tool tip has been updated to state:

    Stay updated with exclusive e-books, timely invitations to webcasts and events and other communications from Golden Helix.”

  • Recent projects that no longer exist are now shaded a lighter gray on the welcome screen and are italicized (except on MacOS) in the File > Recent Projects menu. The missing projects can now be cleaned up or all projects can be removed from the list with new menu options.
  • On Linux and Windows tabbing from the keyboard will now indicate focus in the Data Source Library on panel buttons including Locations, Plot Data and Information.
  • In the Data Source Library, using the keyboard arrows to select a source will now update the information about that source in the Information Pane.
  • Instead of error message will now provide truncated text for Excel export when cell size is greater than 32,767 characters.
  • MacOS Polishes:
    • Keep VarSeq maximized when adding another view to the window.
  • Updated hyperlink in Identifier field to default to the GRCh37 archive for COSMIC identifiers.
  • Modified VCF export options so the default selection is a strict subset of the imported data, not dropping any fields or including any annotation sources.
  • Log View Polishes:
    • Add template series name, version and author to project log if these fields are not empty.
    • If an Alt Read Ratio cannot be computed this information is now reported in the Log View.
  • Clear completed downloads from the download manager after closing VarSeq.
  • Ensure that correct messages are provided that differentiate between sources that need downloading or algorithms that need input. Also, if there are sources that need to be downloaded this message is presented right after opening a project instead of after import or other preceding algorithms are finished.


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