VarSeq 1.4.1 Release Notes

New Features

  • The table has been completely rewritten with multitude of usability improvements as well as improved memory efficiency, removing previous limitations to the number of variants viewable in VarSeq. See the updated Table View section for more details.
  • Drilling down on details in the table has been rebuilt with in-place details about the current cell and row. These details can be snapped to the right of the table and maintain synced with the current row. See more about the new Detail View.
  • When shrinking columns to increase the number visible in a table, we now shorten column names dynamically to their symbol. Thus columns like “Read Depth (RD)” will be shorted to “RD”. Similarly when the space is available the full column name will be used. Note this pertains to “Variant Sets” toggle-fields used to flag variants to report, which previously were “fixed” to their short two-letter symbol form.
  • Previously, the Group by Genes feature had a limit of 65,536 variants being in a single gene. This limit has been removed.
  • Added Aggregate Compute Fields algorithm which allows for summary computations on sample fields. See Aggregate Compute Fields for more information.
  • Added support for Assessment Catalogs hosted on VSWarehouse™ to be utilized by VarSeq.

Bugs Fixed

  • No longer allow sample specific variant sets to be created for projects with no samples.
  • Fixed BAM hyperlinks in Samples table so they will work if the path contains “&” or ”,”.
  • When saving Assessment Catalog fields of type “Multi-Item Select” with more than one selected item, only the first selected item was keeping its selected states. It now saves and restores properly.
  • Fixed behavior in Note tabs where editing the title of an existing note would sometimes indent all the contents of the note.
  • Informative error messages now provided when selecting incorrect sources to be used for subsetting data on the import dialog.
  • Allow for import of VCF info fields that contain a dash in the identifier.
  • Fixed error when selecting TakeAll option for merge behavior on import of variant sites fields.
  • Fixed bug in report template that inhibited auto-downloading of required OncoMD annotation sources.

Polishes

  • Significant speedups can be expected when importing data, especially data with large numbers of samples. Under the hood, new compression algorithms are being used to store project data.
  • The export dialogs have now been rebuilt as wizards with more descriptive prompts and a running log describing the export status. The back end has also been optimized with significant speedups noticeable on large exports.
  • GenomeBrowse views now have a right-hand dock window to display the details of the last clicked item. It also has had the button to add plot items renamed to “Plot”.
  • Clicking the histogram button on a numeric filter card now pops up a drill down on that field include a histogram chart.
  • When a table is sorted, there is now a interactive purple sort indicator beside the filter indicator that allows you to toggle the sort on and off, as well as change its direction and remove it.
  • Sorting a field that is a sample field for the current sample gets updated as the current sample changes. For example, you can sort your table by Zygosity, and as you change the current sample, the table will re-sort on the Zygosity of the newly selected sample.
  • You can now select multiple rows using Shift and Ctrl and toggle the checked state of variants for use in reports and variant sets.
  • While variants are importing, all incoming fields are now immediately visible in the table.
  • You can now interact with fields as they are being computed, including sorting on them and getting their descriptions.
  • The selected gene in a Variant by Genes table is now preserved as the filters are updated, as long as that gene remains in the filtered variant set.
  • Made the fields in the Manage VSWarehouse™ dialog read only.
  • Allow the sample algorithm fields like Zygosity to be deleted.
  • The annotation source selected by default for the region import option is the current RefSeq Genes source for the selected project assembly. Dialog will display source name with the path to the source listed as the tool tip.
  • Updated Human Phenotype Ontology and Gene Ontology annotations sources used with the PhoRank algorithm. See Sample PhoRank Gene Ranking for further details.
  • The import algorithm will now recognize <*> in gVCF files as a spanning alternate allele that can be used to fill in reference calls when importing multiple samples together.
  • Updated sample level fields naming for family samples.
  • BAM file selection for association on import of samples was optimized to better handle files that are stored in different directories.
  • Changed sort order of samples in projects to use use natural string sorting of sample names.
  • The Assessment Catalog view now has a “Refresh” button that allows you to update to changes from the database that occurred since you selected the variant.

Note: Projects created with VarSeq 1.4.1 or newer will not be able to be opened by previous versions. If asked to open a project that is newer than the supported version, VarSeq provides a warning.



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