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.
- 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.
- 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.
- 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.