SVS 8.4.0 Release Notes

This release changes how you access the software. At this time this is an “opt-in” release. To obtain access to the features, bug fixes and polishes listed below, please contact support@goldenhelix.com and let us know you would like to upgrade to SVS 8.4.0!

New Features

  • Meta-Analysis is now available in SVS. See Meta-Analysis for more information.
  • New features for importing variants through the Import > Import VCFs and Variant Files tool, see Import VCFs and Variant Filesfor full details.
    • Now able to import variants from text files provided by 23andMe, see Select Files to Import for more information.
    • Added support for importing gVCF files, see gVCF Conventions for specifications on this format.
    • Added the ability to import tumor/normal pairs, see Select Relationship for more information.
    • To avoid operating system limits on the number of files that can be open simultaneously, the selected files will be batched into groups of no more than 450 files which will then be merged to complete the import.
  • Golden Helix SVS now has a login and register step when first starting the software. If you do not already have a Golden Helix account, you can register and create a login by using the Register tab. Once you login you can remain logged in unless your account does not allow that option. Alternatively, you can logout at the end of each session.

Bugs

  • Fixed the issue with missing counts in the DNA-Seq > Collapsing Methods > Count Variants per Gene tool that occurred when there were non-overlapping transcripts with the same gene name.
  • Fixed issue with Set Genotypes to No-Call based on Additional Spreadsheets that caused the software to crash when tool is started from a spreadsheet that does not contain genotype columns.
  • Convert Wizard bugs fixed:
    • Fixed error when a CSV file was selected for converting that caused the comma delimiter to be treated as part of the field data.
  • Allow GenomeBrowse to plot data from a VCF file that contains string arrays instead of giving the error that mapFields cannot be converted from StringArray to String.
  • Fixed issued that caused Mac OSX menus and menu items for the Spreadsheet Editor to be unavailable.
  • Fixed python annotation type selection to included one, multiple, or all possible types.
  • The Edit > Recode > Recode Genotypes tool will now work correctly for mapped and unmapped genotype data in the same spreadsheet.
  • Confirm that all covariates selected for Predicting Phenotypes from Existing Results are present in the fixed effect coefficient output from K-Fold Cross Validation for Genomic Prediction

Polishes

  • Import > Import VCFs and Variant Filespolishes:
    • Allow the specifying of a field in a sample information text file that contains renamed sample names. This allows the mapping of sample names to new names and fills in the Renamed Sample field in the import wizard.
    • When importing always allow the FILTER option on the Import Summary page regardless of the field merge behavior.
    • Allow for genotype import from VCF files with no explicit GT format field defined in the header of the file.
    • Make it more obvious when an invalid segment is entered into the genomic regions input box and prevent importing until a valid segment is entered or the option is cleared.
    • Report any genomic region subset specified in the Import Wizard in the node change log.
    • Now suppressing progress for applying marker maps to the imported spreadsheets.
    • Provided more informative errors when unable to sort VCF data on import.
    • Trim white space from the sample field information after splitting on the specified delimiter.
    • Allow entity information to be imported from a text file regardless of the amount of samples.
    • Added less strict matching for pedigree fields when importing family information from a text file.
  • Added additional output to GWAS results:
    • Mixed Linear Model Analysisadded:
      • Actual sample size (after removing samples with missing genotypes) for each marker
      • Test (Minor) Allele and Other allele
    • Number of samples (all genotypic and numeric tests)
    • Number of cases and number of controls (all case/control genotypic and numeric tests)
    • Effect Direction, when appropriate one of these statistics is output:
      • Correlation R for most case/control tests
      • Armitage T for the Armitage and Exact Armitage tests
      • Change in the Dependent Average for the F test

      See General Statistics for more information on these statistics.

  • Convert Wizard polishes:
    • Added support for converting BED files with only chromosome, start position, and stop position.
    • Added support for vcf.gz (gzip) files.
    • Added the ability to copy source information from an existing annotation source to a new source through the Advanced Options.
  • In the Data Source Library, using the keyboard arrows to select a source will now update the information about that source in the Information Pane.
  • Clear completed downloads from the download manager after closing SVS.
  • Keep unmapped columns when subsetting visible markers from variant maps and LD plots in GenomeBrowse.
  • Added the option to select the column headers to be used in the Identifier field when exporting data to VCF files.
  • Recent projects that no longer exist are now shaded a lighter gray on the welcome screen and are italicized (except on MacOS) in the File > Recent Projects menu. The missing projects can now be cleaned up or all projects can be removed from the list with new menu options.
  • Gene and Interval annotation results now show all overlapping features in the region and allow for providing all fields from the annotation source or just the name identifier field.
  • Converted and replaced XML properties file with JSON properties file.
  • Cleaned up install to existing directory to remove deprecated library files.


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