1. Home
  2. SVS
  3. SVS Release Notes
  4. SVS 8.7.0 Release Notes

SVS 8.7.0 Release Notes

New Product Add-Ons for SVS Server

  • Genotype Imputation with an adaptation of the BEAGLE 4.1 program is now available with a SVS Server license. See Genotype Imputation for more details.Note: If you are interested in adding the new Genotype Imputation product to your  SVS server license, please contact your account manager or info@goldenhelix.com.

New Features

  • Added PhoRank algorithm to rank genes based on their relevance to user-specified phenotypes. See PhoRank Gene Ranking for more information.
  • Added the ability to recode AB genotypes to AGCT genotypes using the new Recode SNPs to Variants tool. See Recode SNPs as Variants for more information.
  • Premade human reference panels can now be downloaded from the Golden Helix server through Download > Imputation Data. These sources are filtered versions of phased genotype data provided by BEAGLE and are designed to be used with the new Genotype Imputation tool.

Bugs Fixed

  • Fixed issue in Convert GFF3 Files to Annotation Track script that caused multiple transcripts in a single gene to be collapsed into a single record.
  • Fixed subset spreadsheet output for Filter Samples by Call Rate tool that occurred when original genotype spreadsheet was sorted.
  • Fixed the crash that occurred for Genotype Statistics by Marker and Genotype Filtering by Marker when classifying alleles based on Reference and Alternate.
  • Numeric Value Plot item in the spreadsheets GenomeBrowse menu now plots the selected value field instead of just the first column in the spreadsheet.
  • K-Fold Cross Validation using the GBLUP method will now run with a binary trait when selecting more than two iterations.
  • Fixed error with Find de Novo Candidate Variants script that occurred when unchecking the option to treat missing genotypes as reference and multiple families existed in dataset.
  • Updated Import VCFs and Variant Files to better report half-called genotypes with missing alleles.
  • Save as Image functionality now recognizes manual y-range changes when a GenomeBrowse plot is first created.
  • Fixed import of family samples in the Import VCFs and Variant Files tool.
  • Fixed error with Import Impute2 GWAS Files when importing multiple files from the same chromosome and including INFO files.
  • Fixed a packaging issue on Mac that prevented CNAM Optimal Segmenting from being able to run in OpenCL accelerated mode.

Polishes

  • Update export to Variant Call Format (VCF) script to handle half-called genotypes.
  • Random Effects Components are now included in the output for each fold as a part of the estimates by sample when running K-fold Cross Validation.
  • Annotation sources created using the Python API now create files compatible with older product versions.
  • Updated Import VCFs and Variant Files tool to include import of VCF files without sample level information.
  • When exporting data as a VCF file using the File > Save As…> Variant Call Format (VCF)tool, you can now select the alternate field in the marker map to be used to create the VCF file.
Updated on March 9, 2021

Was this article helpful?

Related Articles

Leave a Comment