VarSeq 1.0.4 Release Notes

New Features

  • VCF import now includes the option to merge (or not) files that have the same sample names.
  • Added additional keyboard support, see the Reference section of the Getting Started Guide.
  • Now multiple annotation sources can be selected during Annotate Data Source….
  • Added the Match Gene List annotation algorithm to filter variants based on presence in a specified list of genes. See: Match Gene List for more information.
  • Added support to copy fields from the Table View.
  • Categorical tables are now created for string column reports when there are fewer than 40 unique strings in the column.
  • Histograms and field reports can now be created directly from a numeric filter card by clicking on the histogram icon.

Bugs Fixed

  • Fixed duplication and incorrect ordering of chromosomes on import of some VCF data files into VarSeq.
  • Fixed table row highlighting to have better contrast on Linux.
  • Adding uncompressed files to the import wizard now correctly uses template family settings.
  • Now VCF import properly handles the case of merging files when one or more files have an AF (Allele Frequency field) and one or more do not have this field.
  • Fixed left shifting of deletions on import of VCF files to VarSeq.
  • Fixed left shifting of InDels by one base pair when exporting data to VCF files.
  • Fixed crash on import of data with allelic primitives transformation when:
    • The data is from Ion Torrent
    • Variants are missing alternates, or
    • Have format fields with an incorrect type.
  • Other allelic primitives bugs fixed:
    • Remove common prefixes from the Ref/Alt pairs.
    • Prevent left shifting on insertions and deletions.
    • Reduce Number = “A” fields to values matching the new Alternates list.
  • Fixed crash on left-align for:
    • Multi-allelic sites, or
    • Sites with an invalid Ref/Alt value, or
    • When there is a repeat sequence region.
  • Other left-align bugs fixed:
    • Fixed the overly aggressive stripping of bases on multi-allelic sites.
    • Prevent duplication of records on import of data.
    • Prevent right-shifting of variants.
    • Ensure transformation is insensitive to field reordering.
  • Fixed genotype representation after performing left align and allelic primitives transformations.
  • Made COSMIC mutation ID hyperlinks in the details view individually clickable.
  • Prevent Genotype Zygosity algorithm from adding empty zygosity columns to Compound Heterozygous Variant column groups.
  • Compound Heterozygous Variants and Regions can now be computed without any other filter cards in the filter chain.
  • Disabling a card tracked by a table now updates the table to pass-through the filter value.
  • Fixed crash when deleting a column group in a secondary table while an annotation algorithm is running.
  • GenomeBrowse bugs fixed:
    • Clicking on a folder URL now launches a file explorer window at that location instead of trying to launch and failing.
    • In the Convert Source Wizard, fixed the bug that made the last field invisible in the field edit list when a computed field was added.

Polishes

  • Updated algorithms to handle hemizygous variant calls.
  • Added documentation of how to manually add AppData links for server installs. See Linux Configuration in a Shared Environment.
  • Export to Excel now includes an option to not export hyperlinks.
  • Removed limits on Ref/Alt when exporting to a VCF file.
  • When exporting data to a VCF file, fields with type “A” the field cardinality is read and written to the file so that the fields remain type “A”.
  • Moved the Lock/Unlock action for tables into the filter button in the Table View.
  • Make string table filters and string filter cards case insensitive.
  • Give options for table filtering of Boolean fields (True/False) “==True” and “==False” instead of using numeric filtering options.
  • Allow reordering of source group sub-fields for collated sample fields.
  • Close the source selection dialog when annotation sources are selected from Annotate with Data Source… and Download is clicked.
  • Present a more informative error when running the Group by algorithm on a field when there are more than the maximum number of variants allowed in a particular group.
  • Updates to the Compound Het algorithm:
    • The selected fields for the gene and allele frequency field parameters are now made more prominent and the Cancel button on the allele frequency field selection page was renamed to Skip as clicking on this button does not cancel the algorithm but skips the input of the optional parameter.
    • After computing compound heterozygous variants and regions on the variants in the table, a filter card is added automatically to the Filter Chain.
    • The compound het algorithm can now have different inputs for each affected sample.
  • Made all URLs work as expected.
  • Direct COSMIC ID URLs to COSMIC and RS ID URLs to dbSNP.
  • Compute Alternate Allele Frequency on FreeBayes output using this formula: AO / ( sum(AO) + RO).
  • Add field documentation to the field Hide/Show column and column group dialog.
  • Apply the allelic primitives and left align transformation options used when creating a template on projects created from templates.
  • Add a spin cursor to the filter chain button in the Table View when evaluating a filter chain.
  • Changed default visible outputs of Annotate Transcript algorithm to include Tx Name, CDot, and PDot fields.
  • When creating a project from a template, hide columns from the data not seen in the table in the template.


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