VarSeq 1.3.1 Release Notes

New Features

  • Import more samples or variant sites into a project now available File > Import… when data already exists in a project.
  • Added new algorithms:
    • Count Variants by Gene: Counts the number of homozygous, heterozygous, and all variants per gene.
    • Aggregate Counts per Gene: Counts the number of unique variants per sample group or over all samples per gene.
  • The number of variants per each record set is now visible on filter cards as a tag indicating how many flagged variants pass through the filter. The tags are clickable and also have right-click menus to update the table to the tagged variants.
  • Now prompt with an information icon **Info Icon** when a new version of an annotation source is available.
  • Added a VSPipeline commands:
    • to get the user’s encrypted password
    • to create, set and modify record sets
  • A new mini demo project Example Tumor-Normal Pair Analysis is available by going to File > Open Example Project.

Bugs Fixed

  • Import variant bugs fixed:
    • Prevent gVCF files from consuming linearly increasing amounts of RAM on import which can max out the available RAM.
    • Import unsorted VCF files in the correct genomic order.
    • Fixed Advanced Options on import to allow for moving VCF fields from the variant sites to sample level locations.
    • Prevent crash on import of some “sites-only” VCF files.
  • Prevent crash when running the Genotype algorithm on a VCF file with an additional INFO level “Alternates” field.
  • VSReports bugs fixed:
    • Prevent crash when unlinking hyperlinks in rich text dialogs when configuring report templates.
    • Ensure genes are matched against all OMIM gene name fields (GeneNames and AlternativeGeneNames) to obtain OMIM information for variants in reports.
  • Fixed issue with progress not showing when annotating against a batch source like OMIM genes.
  • Made Save Project as… work when a report view exists in the project.
  • Ensure GenomeBrowse can plot BAM files using Plot Sample Alignment when the path was specified from a sample information file on import.
  • VSPipeline bugs fixed:
    • Make the table wait for complicated filter chains before exporting data to ensure the filter chain is completely finished with all computations.


  • Added field documentation for:
    • Exon number for the Annotate by Transcript algorithm.
    • Mendel Error sample field and algorithm description.
  • Adjusted variant/gene batch annotation for secure sources to perform more queries per batch to increase speed on annotating against sources such as OMIM genes and OMIM variants.
  • Added HTML format flags into annotation Source Editor so visualization of these fields can be improved though HTML formating.
  • Updated dbNSFP voting algorithm to included the new FATHMM MKL Coding Pred for versions 3.0 or higher.
  • Remove unused data files in the project’s data folder on project save.
  • Release file handles after closing a project to remove file locks on project data. This will allow a project folder to be deleted without having to close VarSeq.
  • Changed “Project in use” dialog buttons to be “Cancel” and “Override at your own risk” for clarity.
  • Allow filter cards that are linked to an algorithm input to have their fields changed as long as the source stays the same. For example, you can change the field used in filtering a Compound Het algorithm output.

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