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.


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