VarSeq 1.1.3 Release Notes

New Features

  • New Add-On Features:
    • Integration with MedGenome’s Oncology Mutation Database (OncoMD) to streamline annotating and filtering variants against cancer-specific genetic alterations. See MedGenome OncoMD for further information.
    • VarSeq can now be run from the command line with vspipeline to automate and make workflows accessible in clinical and research pipelines. See VarSeq Pipeline Runner for more information.
  • Added the option to filter variants on import based on the FILTER field based on FILTER values specified in the headers of all VCF files selected for import. If no filters are chosen all variants will be imported.
  • Added support for importing gVCF files, see gVCF Conventions for specifications on this format.
  • Updated Compound Heterozygous Variants and Regions algorithm to include advanced parameter options. Tool now allows de Novo mutation to be used when classifying Compound Het regions and also allows for one missing parent in in the trio.
  • New algorithms (Add > Compute Additional Data…):
    • Frequency Aware Zygosity computes the variant zygosity with a correction based on an alternate allele frequency from a population catalog. See Frequency Aware Zygosity for more information.
    • Mendel Error computes the Mendel Error status for a child’s genotypes given at least one parent. See Mendel Error for more information.
  • Added the ability to inspect and set the view and data user IDs.

Bugs Fixed

  • In the Import Wizard, prevent selection of invalid files when selecting a text file that specifies sample information.
  • Fixed an issue that allowed the last variant of a preceding chromosome to be included in a chromosome segment filter on the Chr:Pos column when reimporting data into an existing project.
  • Ensure that the genome field is set in all project files when created from an empty template.
  • Disabled Histogram plots for fields with all missing numeric data.
  • Fixed issue for Mac OSX when recovering projects saved on mounted drives.
  • Fixed issue preventing importing data into a project saved on a mounted/network drive on Linux and CentOS.
  • Ensure that changes which modify a project can be saved, including:
    • Showing or hiding table columns
    • Changing the current sample
    • Changing the current tab
  • When exporting data as a VCF file, FILTER categories are now properly converted back to an INFO field with multiple FILTER values separated by a semi-colon (;).
  • Expression Editor fixes:
    • Convert computed binary arrays to enumerated arrays.
    • Prevent crashes caused by MuParserX from trying to convert floats or doubles to integers.
  • On RHEL removed do not create a QtProject.conf file which can result in a file lock erroneously.

Polishes

  • Updated default RefSeq gene annotation source based on GRCh37_g1k build to include Locus Reference Genome (LRG) identifiers, updated source name is RefSeq Genes 105v2, NCBI.
  • Updated Annotate Transcript by including the use of canonical transcripts to create clinically relevant annotations.
  • Update Count Allelesalgorithm:
    • Added # Alleles to the Count Alleles algorithm. This contains the total number of observed alleles in the called genotypes (plus two for each missing genotype). This number is the denominator used to calculate Allele Frequencies.
    • Added missings category counts for grouping variable if present in samples.
  • Made outliers visible by default for Histograms plots and adjusted outliers button to be consistent with other hyperlinked text.
  • Import Wizardpolishes:
    • Only disable the option to append records after at least two sources have been added that do not have the same samples in both files.
    • Allow for more values to be detected as Affected/Unaffected when specifying sample information from a text file. These values include:
      • Affected: true, t, 1 (case insensitive)
      • Unaffected: false, f, 0 (case insensitive)
    • Allow the specifying of a field in a sample information text file that contains renamed sample names. This allows the mapping of sample names to new names and fills in the Renamed Sample field in the import wizard.
    • Providing more informative errors when there are write permission issues to the folder where the data is stored.
    • Allow for genotype import from VCF files with no explicit GT format field defined in the header of the file.
    • When there are site and sample level fields with the same name merging of data between the two is no longer done when sites fields are moved to sample level fields on import, instead separate fields are created to maintain unique data entries.
  • Updated the Database View to immediately use the current variant.
  • Exportpolishes:
    • For VCF files only:
      • The matrix filter field now uses the identifier “FT” as per the specification
      • The messages from the VCF write are now shown at completion
      • On completion of the export, the dialog now has the option to open the folder where the file was written.
    • The dialog for the final step of the write dialog are now smaller and fit the content.
  • Add information into the license activation dialog (Help > Activate a VarSeq License Key) that lists any add-ons included with the license.
  • Update Group By algorithm to maintain current visible columns from the variant table in the new secondary table view.
  • Expression Editor polishes:
    • Removed matrix functions that have no function in VarSeq
    • Renamed strlen, strsplit, joinlist functions to the more common len, split and join functions.
    • Polished function documentation to be more useful and have more consistent descriptions.
    • Added string concatenation button
    • Provided functions that operate on array types, for example sum(array) will provide a sum of the list of numeric values in the array.


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