VarSeq 1.2.0 Release

New Features

  • Added the ability to lock a filter chain and the ability to create a template with a locked filter chain to prevent changes to the filter chain after it is locked.

Bugs Fixed

  • Report one clinically relevant transcript per gene in a region instead of one all genes that overlap a variant.
  • Prevent crash when logging out while downloading sources from the Public Annotations data repository.
  • Proxy settings are now saved correctly for all platforms.
  • Import bugs fixed:
    • Fixed import of 23andMe samples that were previously imported or converted to TSF files.
    • Use original sample names for matching with sample information from a sample field/information file even if the sample names have been renamed in the Import Wizard before loading a sample field/information file.
    • Variants are now correctly sorted in genomic order when imported with the advanced Allelic Primitives options selected.
  • Present correct error when trying to perform computations on a source and at the same time plot the source in GenomeBrowse instead of updating the time remaining for the completion of the task.
  • Prevent crash when the current sample is set to an unaffected sample and the table includes PhoRank and you try to display only “Affected Samples”.
  • Make sure that at most 65530 links are created when exporting XLSX files to prevent Microsoft Excel from treating the file as corrupted.
  • Variant Databases no longer expects the Ref/Alt column to be the second column in the table, this bug caused variant databases to get in an unusable state.
  • Merging TSF files in the Convert Wizard now correctly merges the segment list.


  • Filter containers now display the first error message generated by the filters within the container. The filter view also displays the first error message at the bottom of the view. This prevents error messages from being hidden within collapsed cards.
  • Ensure that filter cards for samples specified by relationship to the current sample (Mother/Father/Normal) display errors when the specified sample label is not found.
  • No longer creating lists for certain variant sites fields when importing a single VCF file.
  • Removed rich text from filter card titles and template documentation. This ensures consistency when opening a project or template across various operating systems.
  • Fixed placement of top left stash button when the toolbar is hidden.
  • Added parameter sample_fields_renamed_col to the import command for VSPipeline.
  • No longer including file merge information when a single variant source is imported.
  • Now a primary view window is tracked. This is the only window that will have the global toolbar. Closing non-primary views will just close that view. Closing the primary view will prompt for save action and close VarSeq.
  • Allow multiple instances of VarSeq and other Golden Helix products to download files from the Data Source Library simultaneously.

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