Software Update Archives - Page 3 of 3 - The Golden Helix Blog

New Algorithm: Variants Matching Current Sample

New Algorithm: Variants Matching Current Sample

Those of you who have been attending our recent webcasts have learned about our upcoming VarSeq release. A part of that release will be an additional algorithm that will annotate variants matching the current sample. If you are not familiar with these webcasts, here are several on-demand webcasts I recommend…

Upcoming VS-CNV Update: CNV Event Reporting with ACMG Guidelines

Golden Helix is excited to release an upcoming VSClinical feature that allows users to analyze next-generation sequencing (NGS) CNV event reporting with ACMG guidelines. This feature will be the first in the NGS workspace to allow this capability and if you are curious about the functionalities you can get a…

SVS 8.9.0 Release Notes

Eigenvalue Decomposition

SVS 8.9.0 was released on August 19th and features a new GBLUP by Bin feature and a new utility to find the LD scores of markers and categorize them into bins, along with several mixed-model upgrades and many other upgrades, fixes, and polishes. The two new features LD Score Computation…

Coming to SVS: LiftOver Capability

The world has been making a shift to use GRCh38 human genome reference coordinates, but the transition has not been fast. Many of the mainstay human catalog projects are changing to use native GRCh38 catalogs, or are remapping their current data to GRCh38 coordinates. While this seems to be the…

CADD Scores: New and Improved CADD v1.4 and CADD v1.5

The University of Washington’s Combined Annotation Dependent Depletion (CADD) algorithm, now available in CADD v1.4 and CADD v1.5, measures the deleteriousness of genetic variants. This includes single nucleotide polymorphisms (SNVs) and short insertions and deletions (indels) throughout the human reference genome assembly. This algorithm was introduced in 2014 and has since become…

Updates to Default Transcripts and Gene Preferences in VarSeq

An under-appreciated area of complexity when looking into the field of genetics from the outside can be found in genes and transcripts. Alternative splicing allows eukaryotic species to have a wonderfully powerful genetic code, resulting in multiple protein isoforms being encoded in a single section of DNA. But when it comes to…

Detecting de Novo Copy Number Inheritance and Family Segregations

In trio workflows, one of the most important factors in scoring a variant is understanding how that variant is inherited from the parents. Likewise, when looking at extended families, the segregation, or presence of the variant among the affected versus unaffected individuals provides evidence for its pathogenicity for a given…

VarSeq 2.2.1 Release Notes

ClinVar

VarSeq 2.2.1 was released on April 1st and features an upgraded gene annotation capability with new RefSeq genes tracks and an AMP workflow addition: the Drugs and Trials tab. The new RefSeq human genome genes tracks contain updated gene names and the recognition of any MANE (Matched Annotation from NCBI…

VarSeq 2.2.0 Release Notes

ClinVar

VarSeq 2.2.0 was released today and this a stable release full of upgrades and polishes. Some of the newer features include the ability to store and include AMP Cancer assessment catalogs on VSWarehouse, quicker accessibility to common annotations plotted in GenomeBrowse, and the addition of all of our standard templates…

SVS 8.8.3 Release

gene ranking

The SVS 8.8.3 release was created to incorporate some of the CNV, genome assembly control, and splice site capabilities that are present in VarSeq, as well as clean up and streamline the GWAS workflows (like when using Mixed Linear Model algorithms) for a better user experience. New Product Add-Ons for…