VarSeq 1.4.6 Release Notes

New Features

  • The Count Alleles has two additional optional parameters. The first adjusts the denominator of the allele frequencies to remove samples with explicitly marked No-Call genotypes (values of ”./.” in the GT field) and similarly report only called genotype samples in the “# Alleles” field. The second enables an optional Sample Names field output that reports the names of the samples that contain variant genotypes for rare variants.

Bugs Fixed

  • For new projects created in VarSeq 1.4.5 that ran the Coverage Statistics, LoH or CNV algorithms, the new per-sample outputs for these algorithms where showing up in the per-sample groupings of Variant tables. They are now back to being displayed under their own source grouping as was the behavior in 1.4.4 and earlier. You may need to close your Variant tables and re-create them to reset the table configuration to the correct behavior.
  • The VSReports API results for querying the current selected variants sample-based fields such as Zygosity and Genotype Quality had a regression in 1.4.5 and returned null results. This has been resolved.
  • When relative BAM paths were specified on a project created by Windows and subsequently that project was opened on Linux or Mac, the relative file paths were not resolving. Paths are now saved in a platform-independent manner.
  • Fixed an issue creating a custom annotation track from a VCF when a URL template was specified for one or more fields.


  • The CNV state plots created from the CNV algorithm output table will draw in a itemized mode with color even when zoomed out to the whole genome level. Other region plots switch to a gray histogram plot mode at a multi-chromosome zoom level.
  • The coverage statistics algorithm maximum detectable depth has been raised to 500,000 from 100,000 to accurately profile very high read depth regions.
  • For the Loss of Heterozygosity (LoH) algorithm, the detected three copy state has been renamed to Trisomy (previously Triploid).
  • To improve usability, the table does not pop-up a tooltip style details window after clicking by default. Top open the pop-up details on the last clicked table item, toggle the details pane on the table toolbar and click the “Undock” icon next to the close button in the upper right.

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