SVS 8.4.1 Release Notes

IMPORTANT: This is a major update and will completely remove and reinstall SVS to the specified install folder. If you have any user data, annotation sources, projects, notes, etc. in the SVS Program folder please back them up and move them to a different folder. If this is not possible, please contact support@goldenhelix.com for help with the upgrade.

For information on how to register and activate an SVS License if you are updating from an existing SVS version other than 8.4.0, please click here. To update from SVS 8.4.0 please download a new installer.

New Features

  • Added support for Gene x Environment (GxE) Interaction terms in Numeric Regression. See Numeric Regression Analysis for more information.
  • Added option to center genotypes for Bayes C/C-pi.
  • When in viewer mode have a link on the welcome screen to access example projects.
  • Added the ability to plot a 3D Scatter Plot for numeric data with an optional grouping variable. See Scatter Plot 3D for more information.
  • Now computing an overall Odds Ratio and confidence interval for Meta Analysis. Also added PP/QQ output option to the log output.
  • Updated the software updater which will now download updated files faster and allow for installation of the update at the same time or at a later time.

Bugs Fixed

  • Double-clicking on a GHP project file now launches SVS and opens the project. If you are not logged into SVS you are first asked to login.
  • Merging TSF files in the Convert Wizard now correctly merges the segment list.
  • Do not output major and minor alleles when performing Genotype Principal Component Analysis.
  • Show DNA-Seq and RNA-Seq menus on MacOS X for spreadsheets with and without genomic marker maps applied.
  • Fixed crash when outputting the clusters of runs for ROH.
  • Fixed crash when closing SVS with the Data Source Library open.
  • Fixed Y-axis zoom in GenomeBrowse when not in automatic mode.
  • Enabled access to Proxy Settings when not logged into SVS.
  • Fixed sting list fields in dbNSFP matched variant report.
  • Fixed computations of visible haplotype blocks in LD Plot window.
  • Fixed typo in the Meta-Analysis documentation for the sample-size-based approach. Φ^-1 was described as being “the inverse of one minus the probability density function of the normal distribution when it should be “the inverse of one minus the cumulative distribution function.
  • Fixed searching indexed fields in GenomeBrowse when annotation sources are loaded from Public Repository.

Polishes

  • Allow multiple instances of SVS and other Golden Helix products to download files from the Data Source Library simultaneously.
  • Added the following 3rd party licenses to the about dialog: asa136, newmat, and boost.
  • Converted movable toolbars to fixed “flow” toolbars for GenomeBrowse and adjusted the order of some toolbar items.
  • Added option to inactivate missing values in the Activate by Threshold column tool.
  • When applying marker maps to a spreadsheet a successful completion message will show before the final spreadsheet becomes visible to guarantee the new spreadsheet appears as the top view.
  • Sample size warnings added to Identity by Descent Estimation, GBLUP Genomic Relationship Matrix and Bayesian Genomic Prediction tools that provide a warning that the tool may not finish if there are too many samples in the dataset.
  • On Lin64, renamed libstc++.so.6 to libstdc++.so.6.rename-if-needed so that SVS will run on Ubuntu 15.04.
  • Allow offline activation of SVS license when server connection is refused by local network.
  • Joining, Merging and Appending spreadsheet tools now have the option to allow for case insensitive matching for row labels and column headers.

Registering and Updating License from a Previous Version of SVS

 

Registering

If you do not already have a Golden Helix account from either Genome Browse or VarSeq, click on the register button and fill out all of the required information to create an account.

Activating License

If you had an existing SVS license and you are updating from a version prior to 8.4.0 you should have a key ready for you to activate. Either click on the “Activate License Key” in the lower right hand side of the Welcome Window or go to Help > Activate a SVS License Key. There should be a key entered in already. You just need to click Verify, accept the EULA and then click Activate. If you have problems with this step please contact support@goldenhelix.com.

If you did not have an existing SVS license and were not provided a key please contact support@goldenhelix.com.

 



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