**DNA-Seq > Variant Classification** has been replaced by the new DNA-Seq > Annotate and Filter Variants tool. (See Annotate Variant Effect on Transcripts for further details.)
- New Secure Annotation sources available:
- The previous Annotate and Filter Variants as well as Variant Classification methods have been replaced by a new wizard under DNA-Seq > Annotate and Filter Variants. (See Annotate and Filter Variants for more information).
- Added File > Add Alternates to Marker Map to allow user to add an alternate allele field to the marker map of the current spreadsheet. This field is required for the new variant annotation tool.
- Fixed issue with Mixed Linear Model Analysis and Mixed Linear Model Analysis with Interactions when adding genotypes as covariates to the model.
- Included variant collapsing transform to Import > Import VCF and Variant Files tool to fix issue with duplicate column entries.
- Renamed GenomeBrowse button and menu item to add plots to “Plot”.
- Made several usability changes to the Import > Import VCFs and Variant Files tool including the following:
- The annotation source selected by default for the region subset option is set to the current RefSeq Genes source for the specified project assembly. The dialog will also display source name with the path to the source listed as the tool tip.
- The import algorithm will now recognize <*> in gVCF files as a spanning alternate allele that can be used to fill in reference calls when importing multiple samples together.
- Updated sample level fields naming for family samples.
Note: If you are interested in using the new Secure Annotation sources, contact Golden Helix support or your account representative directly. These are enabled as add-on features to your license.