VarSeq 1.3.6 Release Notes

New Features

  • CADD variant scores are now available in VarSeq. See CADD for more information.
  • Added Variant PhoRank algorithm to rank genes based on their relevance to user-specified phenotypes for all samples. This algorithm will also work in projects without any sample information. See Variant Phorank.
  • VCF export option now supports and defaults to compressed file format.

Bugs Fixed

  • Prevent crashing when trying to plot sources that are not available including:
    • Plot Unfiltered Variants
    • Plot Numeric Field…
  • Fixed bug that triggers unnecessary dialog pop up when Add button is clicked.
  • Fixed an issue that prevented sort order from being updated when record values were changed. To update the sort order, reselect the sort option from the right-click menu.
  • Fixed issue exporting Coverage Region table for multiple samples in the project.
  • Respect all field merge options when importing data from a template.
  • When template contains a computed field that depends on another computed field, wait for the first to complete before starting the second.
  • Fixed bug for computed fields when converting Float64 variables to Float.
  • Fixed progress in convert wizard when left align is turned on.
  • Prompt for download when using Add > Computed Data > Annotate Transcripts and Add > Computed Data > Annotate Regions instead of annotating against the remote source.
  • Fixed issue downloading network sources during batch workflows in VSPipeline.
  • Handling of multiple genotype calls for a single sample at a position has been updated to be more representative of the variant changes. These updates include:
    • Allelic primitives now sums the allelic depth when collapsing two matching (complimentary) features at the same position for the same sample.
    • Allelic primitives now does not sum quality metrics such as read depth when combining alternates to make a homozygous variant genotype.
    • When multi-allelic sites are split on import, use all valid alternate alleles at that site when counting alleles in the Count Alleles algorithm.
    • Include all alleles present in a trio in the Alternate allele list including the alternates not present in the proband.
  • When left-aligning and splitting variants into allelic primitives, merge phased heterozygous calls into a single homozygous call when collapsing the variants.
  • Fixed bug that causes VarSeq to crash when selecting sample fields visibility if sample fields were not imported.
  • Fixed issue with missing report fields from the ACMG Hereditary Gene Panel Template.
  • Allow Evernote to open a new note even when it cannot authenticate a shared notebook. Only show notebooks that can be authenticated in the available list.
  • Fixed the human GRCh_38 assembly so each chromosome had the correct length specified.
  • Fixed issue when importing variants from a TSF file and selecting to subset the import by region.
  • Fixed issues with computing lengths of chromosomes when converting FASTA data to create a new genome assembly.

Polishes

  • Renamed computed “Alt Allele Freq” field to “Var Allele Freq” to ease confusion with the “Alternate Allele Frequencies” in population catalogs. The Var Allele Freq field is computed off of read depth statistics provided by the variant caller.
  • Reuse “Group by Genes” algorithm if available for PhoRank this prevents extra group by genes columns and keeps all associated algorithms on the same axis.
  • Add Cancel button to Plot Numeric Field dialog.
  • Added deprecated flags to the Data Source Library so older annotation sources could be hidden automatically when the current box is checked.
  • Allow download of OMIM and CADD secure remote sources if licensed to use those sources.
  • Added optimization to Count Alleles algorithm to improve speed for large sample sizes.
  • Optimized VCF export for large projects that are filtered to a small set of variants.
  • Turned on Allelic Primitives by default for all import types.
  • Allelic Primitives updates:
    • Now performed before Multi-Allelic splitting.
    • Adds phasing information when a variant is split into multiple variants.
  • On Linux and Mac OS X, import 1/(4^{th}) of the maximum number of open file handles allowed. Changing this parameter for the operating system allows the user to increase the maximum number of file handles for a more efficient import process. For help increasing the soft-limit on Linux, RHEL or Mac OS X contact support@goldenhelix.com.
  • Updated Template Import to support the following:
    • Save deletion of fields during sample import
    • Save filter selection during sample import
    • Save and use subset by region during import
  • Updated verbiage and default options on version update dialog.
  • Updated Count Alleles by Gene documentation.


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