VarSeq 1.4.2 Release Notes

Note: If you are interested in adding the new CNV Caller on Target Regions product to your VarSeq license, please contact your account manager or info@goldenhelix.com.

New Product Add-Ons

  • CNV calling on NGS target data is now available as an add-on licensed product to VarSeq! In it’s initial release, we are recommending it only for the application of targeted gene panels on NGS data. It will run with Exomes, but it is expected that further tuning and region-specific adjustments may be needed. See the CNV Caller on Target Regions section for more details.

New Features

  • The new CNV calling algorithm is introduced in this release. In it’s initial release, we are recommending it only for the application of targeted gene panels on NGS data. It will run with Exomes, but it is expected that further tuning and region-specific adjustments may be needed. See the CNV Caller on Target Regions section for more details.
  • You can now plot sample-level fields imported with your VCF or from the output of algorithms (such as the CNV algorithm) and have the values track the project Current sample. This dramatically improves many interpretation work flows that utilize a GenomeBrowse view.
  • String and Enum fields can be plotted directly. Enum fields will automatically be colored by their values.
  • Sample-level fields for variants or other tables with genomic coordinates such as Target Coverage or CNVs can now be plotted as a Heat Map for all samples using the new “Plot for All Samples” context menu on their columns.
  • All fields can now be searched using the “Query Column Values” context menu item. This makes it easy to filter non-variant tables (such as the new CNV events table) on things like the CNV State field. You can also search the genomic position or range column at the table level.

Bugs Fixed

  • Importing variants into a configured Assessment Catalog resulted in errors when the input source contained indels.
  • An issue where the bottom two rows of a table did not allow copying of the cells content to the clipboard was fixed.
  • Progress reporting was fixed for XLSX export in VSPipeline.
  • Table filters are now case insensitive. In the previous 1.4.1 release they were made case-sensitive unintentionally.
  • Fixed issue using the split function on string array fields within the Expression Editor.

Polishes

  • The context menu for column groups now supports immediate toggling of the field visibility of the fields for the given source. This feature was available in 1.4.0 in a different context menu and didn’t make it into the table replacement that shipped in 1.4.1. The new implementation handles sources with many fields compactly and easily supports toggling all fields on or off.
  • Selecting multiple rows of the variant, coverage or CNV table will zoom the GenomeBrowse view to include all the selected genomic features.
  • You can now import VCF files with no records in them as well as export empty tables. This comes in handy when dealing with small gene panels on a project-per-sample basis.
  • The log for the import algorithm now displays the common base path of imported VCF files.
  • Updated family import options for multi-allelic splitting to reduce duplicate variant data being created.
  • When out of date annotations are updated, they now retain their position in tables in which they are visible.


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