Add-On Scripts & Data Repository

When the Transcript Disagrees with the Genome

Oct 8, 2026

A transcript’s reference sequence does not always match the genome assembly beneath it. Even a one-base difference can shift downstream coding coordinates, alter a codon, or change a variant’s predicted effect. VarSeq 3.1.0 accounts for these differences directly. The new RefSeq Genes track records the exact differences between curated RefSeq…

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Considering Data Quality: From Sequencing to Reporting

Dec 11, 2025

When quality metrics generated during secondary analysis are not incorporated into interpretation and reporting, variants are reported without the important context that could affect confidence in the call. The Golden Helix software suite has been designed to help you bring in quality metrics from secondary analysis through to interpretation and…

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Challenging Genomic Regions: Paraphase Integration in VSWarehouse 3

Dec 9, 2025

Short-read sequencing often fails to capture clinically actionable information from challenging genomic regions. While long-read sequencing now enables accurate and comprehensive detection of complex variants, there are still regions of the genome that remain notoriously difficult to analyze. Unfortunately, many of these regions contain genes that are highly relevant to…

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November Webcast: Simplifying Complex Cancer Data into Actionable Knowledge

Nov 6, 2025

As precision oncology evolves, clinicians and laboratories need tools that can both handle massive genomic datasets and translate those findings into clear, clinically actionable guidance. In our recent webcast, “Simplifying Complex Cancer Data into Actionable Knowledge with Golden Helix CancerKB,” we walked through how Golden Helix CancerKB can take clinical…

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Genomenon’s Mastermind – Novel Splice Variant in PAH

Oct 16, 2025

As whole-genome sequencing becomes routine in clinical practice, variant interpretation remains both the opportunity and the obstacle. VarSeq users can efficiently process and report individual samples using extensive annotations and automated classification tools—but even the most comprehensive databases can leave gaps. Some variants simply aren’t found in ClinVar or ClinGen,…

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The Breakend Catalog Format for VarSeq 3

Jul 8, 2025

New to VarSeq 3 is support for breakend catalogs. Breakends represent the junction points of structural variants, which include complex genomic rearrangements like translocations, inversions, and large deletions that play crucial roles in cancer genomics and rare disease analysis. These catalogs are unique as they must save two genomic positions…

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The CoLoRS Database: Enhancing Your Long-Read Sequencing Analysis

Jun 17, 2025

Here at Golden Helix, we continue to develop top-quality bioinformatic software to support high-throughput clinical next-gen sequencing pipelines, including long-read whole-genome-sequencing (WGS) workflows. WGS long-read technologies like PacBio HiFi and Oxford Nanopore offer improved variant calling for SNVs, Indels, structural variants, tandem repeats and repeat expansions, and epigenetic modifications. Each…

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You Might Not Need Citrix

May 8, 2025

Your Genomic Analysis Platform Already Solves Remote Application Delivery Delivering enterprise applications to users is a solved problem, and for many organizations, that solution has been Citrix. It’s the de facto choice for centralizing and securing remote application access, especially for Windows environments. With the right IT support, it gets…

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Evaluation scripts in VSPipeline: We heard you like automation…

Sep 12, 2023

…so we added some automation to your automation so you can automate while you automate! Automation has been a hot topic recently and for all the right reasons. As we (proudly) watch our customers increase their sample and data volume, we are constantly seeking to provide tools to reduce click…

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Versatile NGS Exports with VSClinical’s Custom Scripts

Aug 10, 2023

Configuring a bioinformatic pipeline to reliably process genomic data — particularly at the tertiary analysis stage — is no small task. Doing so in an efficient, consistent way is an even grander challenge. Luckily, the VarSeq software suite provides a comprehensive toolbox for automation and integration. One of the first…

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Specifying Inputs for Reproducibility

May 11, 2023

A new VSPipeline command, set_data_folder_path, designed to bolster consistent input usage. By introducing this innovative command, we aim to empower users with improved data organization, flexibility, and standardization for their clinical cases and analyses. Embracing this command will not only support reproducibility but also ensure accountability, ultimately paving the way…

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Orphanet Annotations in VarSeq

Mar 18, 2021

Orphanet is a public database available in VarSeq that aims to improve the current understanding and treatment options for patients affected by rare diseases. This resource was established in France in 1997 and has gradually grown to cover a consortium of over 40 countries in Europe. The primary goal of…

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New Annotation: GnomAD – Gene Constraints

Feb 10, 2021

VarSeq recently received major upgrades in a wide range of areas, one of these areas includes adding annotations such as GnomAD. This includes new fundamental methods of CNV ACMG guideline processing but also a large number of small additions in annotations. One addition is the application of gnomADs – Gene…

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New Feature in VarSeq: Latest Sample Assessment Algorithm

Jan 26, 2021

In continuation of our blog posts focusing on new features of VarSeq v2.2.2, here we will discuss the Latest Sample Assessment algorithm for both single nucleotide variants (SNVs) and copy number variants (CNVS). This algorithm annotates the variants of the project with the latest assessment from your variant catalog, which…

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New Algorithm: Variants Matching Current Sample

Nov 12, 2020

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…

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Annotate Your VarSeq Projects with REVEL

Oct 6, 2020

Typically, researchers are looking for rare variants in their next-generation sequencing datasets. However, most of the nonsynonymous variants have unknown significance because there is an inherent difficulty in validating large numbers of rare variants or even detecting rare variants with high statistical power. In lieu of this issue, computational tools…

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Updates to dbSNP 154 v2

Sep 3, 2020

In the 1990s the genetic industry voiced a request for a variant catalog that incorporates associated variant information such as phenotypic and metabolic pathways. The call was answered by NCBI, which created dbSNP; dbSNP became publicly available in 1998 and around 1.5 million variants. Fast forward to the present and…

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Kaviar and Allele Frequency Aggregator (ALFA): The Databases You Didn’t Know Existed in VarSeq

Aug 4, 2020

In the search for disease causing mutations it is important to determine if the variant has been previously observed in humans and at what frequency. With the advent of increasing genomic information, there is now a variety of different databases and annotation sources that can be utilized. For some, this…

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How we’re curating OMIM: It’s not as easy as you think

Feb 13, 2018

Relating human phenotypes to genotypes is the name of the game with OMIM, and as their website says, “is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine.” The Online Mendelian Inheritance in Man (or…

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Using GRCh38 for Clinical Interpretation: Now Possible with Our Custom LiftOver Tracks

Jan 23, 2018

There are many good reasons why the pursuit of the highest quality genomic interpretation would lead you to the latest human reference. It is more complete and fixes incorrect or partially missing genes that have known implications for human disease. While most major projects cataloging human populations have plans to…

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