VarSeq 1.4.4 Release Notes

New Product Add-Ons

  • The VS-CNV 2.0 algorithm is now available as an add-on licensed product to VarSeq! Building on the first version probabilistic model for calling CNVs on targeted gene panels, version 2.0 now scales to calling large events and chromosomal aneuploidy events on large gene panes and exomes. Included in this the ability to call Loss of Heterozygosity (LOH) events and integrate those calls with the CNV algorithm. See the CNV Caller on Target Regions and LoH Caller sections for more details.

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

New Features

  • The PhoRank algorithm has been updated extensively to improve the ranking of genes relevant to sample phenotypes. Also, input phenotypes have been extended to include OMIM provided syndromes and phenotypes. The OMIM content add-on is required for this feature.
  • A new Match Gene List from Phenotypes algorithm is available that allows you to define a gene list using input phenotype terms. This also now supports input terms in OMIM as well as HPO. (see Match Genes Linked to Phenotypes)
  • A number of updates and improvements have been made to the gene annotation algorithm that provides per-transcript variant interactions.Algorithm
    • New fields in the Transcript Interactions source provide the reference and alternate Amino Acid for each transcript in the interactions table. Additionally the number of exons and amino acid position are provided.
    • The HGVS p. field was updated for synonymous and frameshift variants to be the long form. For synonymous variants, this includes the reference amino acid. For frameshift variants this includes the amino acid in the altered sequence.
    • Intronic variants now have their nearest exon reported in the Exon Number field, and a new field 5’ Exon Number can be used to determine which two exons the intronic variant is between.
    • In the case where a variant overlaps multiple genes, the order of the genes is consistent between all fields in the Summary source.
  • For VSReports a number of improvements have been made to improve customization. See Customizing Reports for more details.
  • Included new VSReports template that can be used to facilitate N-of-One submissions.
  • A new Recently Closed Tabs menu allows you to reopen tabs you have closed during the current VarSeq session. Right clicking on any tab or tab bar location allows you to access this menu.
  • Variant sets and other table record sets can now have the last change reverted. For example, in the right-click menu over the check-boxes as well in the tool bar menu there is now a Undo last change to Primary Findings.
  • The “Web Browser” tab of VarSeq has been upgraded to be based on the open source version of Chrome. It now has a direct page Print capability, integrated downloads, better session management and overall performance improvements.

Bugs Fixed

  • VCF import updates:
    • Better handling of indels with a reported END field specified.
    • Fixed issue when field promotion was specified along with advanced left-align options for multiple sample import.
    • The Allelic Depth field is no longer an allele matching field unless it is a list.
    • The Variant Allele Frequency is now automatically computed upon the import of TCGC data.
    • Allow for computing the Variant Allele Frequency on a subset of samples that have data to support the calculation.
    • Now able to correctly handle VCF files with an INFO level Samples field included in the data.
  • The max operator in the Expression Editor was not functional when no score was assigned to a variant. Now the Max operator checks for missing values before taking the Max.
  • Fixed issue with Aggregate Compute Fields algorithm when using the length function on a matrix string field.
  • In the Expression Editor, missing string array values are now correctly returned as the correct NA value for invalid expressions. This will now allow users to add expressions such as split(HGVScName[0],”.”)[0].
  • Now correctly saving custom visibility options for sample fields when project is opened or a table is cloned.
  • Fixed naming issue for XLSX tabs when exporting multiple tables in VSPipeline.
  • Fixed an issue preventing annotation tracks to be exported as text files from the Data Source Library.
  • Export of Assessment Catalogs from the Data Source Library no longer contain a blank first row.

Polishes

  • A number of improvements were made related to selection of variants and samples in tables including:
    • Variant selection is now synchronized across tables. If multiple tables contain a given variant, changing the selection in one tables will select that row in the other table. This works for other table types like Coverage, Genes and CNV as well.
    • When a variant or CNV is selected and a GenomeBrowse view tab is open, a blue highlight marker is placed over the genomic interval defined by the variant or CNV. This is similar to existing mouse-anchor selection that spans all plots but is done automatically and is visually distinct.
    • Changing the current variant clears the GenomeBrowse console view so it can not be misinterpreted to be related to the now updated plot views.
    • The Assessment Catalog view relies on the selection of the current variant. Previously it would show out-of-date variants when a change of sample results in the current variant not being selected. It now clears to no variant selection in sync with the table.
    • The sample selected using the project toolbar selected is automatically selected in any open Samples table.
  • Display name for tabs can now be renamed from the right-click context menu for the tab.
  • Improved automatic association of BAM files to VCFs upon data import. Included the option to browse for BAMs for each sample through the file explorer.
  • Project Templates that plot coverage statistics in the GenomeBrowse console view from the Targeted Region on Coverage algorithm will automatically reload the plots in the GenomeBrowse console upon data sync.
  • Decreased the buffer size when importing variants to the Assessment Catalog for a smoother progress bar upon import.
  • When display names have been updated these new identifiers will be included in the Export dialog to create unique entries.
  • Creating a new Variant Set in a project with hundreds of samples now completes in a reasonable amount of time.
  • Added new context arguments thisForm, and varInput to the variant-level autofill function for current variant input context. This allows one form field to respond to changes from another form field in VSReports.
  • Modifying the checked state of a Variant Set and updating entries in an Assessment Catalog now produce useful log messages about the change in the project Log tab.
  • The Plot BAM for Current Sample option is now properly hidden if BAM files were not associated upon data import.
  • Updated the ACMG gene list included with the Exome Trio Template to include genes from the ACMG-SFv2.0 recommendation list.
  • The export to VCF tool now creates compressed vcf.gz files by default.
  • An error will notify users when Split Variants Based on Unique Genotypes is selected as an advanced import option if the required Genotype field is not present in the data.
  • Coverage Region updates:
    • Sample name will now be appended to column group name when output is first generated.
    • Algorithm will now run on multiple cores.
    • A new “Mean Filtered Depth” field, which can be used to detect targets with high level of filtered coverage due to read multi-mapping.
  • You can CNV Reference Folder from the Options dialog of VarSeq as well as from the algorithm options for the CNV Caller.
  • Export to Excel now includes the option to choose a custom delimiter for lists.
  • When closing a project, you will be prompted for any un-saved reports or assessment catalog changes to be saved. This includes reports or catalogs hosted on VSWarehouse.


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