Category Archives: How To’s & Advanced Workflows

Visualization With IGV

         June 5, 2025

Modern genomics workflows often require multiple specialized tools working in concert. In the upcoming VarSeq release, we are excited to announce the option for tighter integration with IGV. Genomics researchers and clinicians are well-versed in using IGV as a visualization tool for their genomic data. This new option will allow for synchronizing the view in the Golden Helix GenomeBrowser with… Read more »

Importing External PGx Calls for Extended Gene-Drug Reporting in VarSeq

         May 27, 2025

Pharmacogenomic (PGx) analysis empowers researchers and clinicians to tailor drug therapies based on a patient’s genetic profile, but not all regions of the genome are easy to interpret. Genes like CYP2D6 and HLA-A are tricky when it comes to rendering diplotype calls. This is due to a number of factors including high polymorphism, structural variations (including copy number variants), and… Read more »

Customized Auto Variant Interpretation in VarSeq

         May 15, 2025

The VarSeq platform has been on the market for over a decade and has established itself as robust and powerful clinical-grade bioinformatics software. Its usage spans many types of analysis, including pharmacogenomics, rare disease, hereditary cancer, somatic, carrier risk, and trio/family. Fundamentally, users have the freedom to build any workflow they need, which is a significant value proposition compared to… Read more »

Sample Catalogs in VSWarehouse 3

         April 17, 2025

Creating and managing sample manifest files in VarSeq has traditionally been a time-consuming process that demands precision and attention to detail. The upcoming VSWarehouse 3 release will feature the ability to use catalogs to save and load sample fields in VarSeq projects. Not only will this allow for easy population of sample fields in VarSeq, but it also has the… Read more »

Best Practices for Variant Annotation and Filtration – Germline Variant Analysis

         January 14, 2025
Best Practices for Variant Annotation and Filtration - Germline Variant Analysis preview image

Golden Helix field application scientists curate a set of FAS templates that capture best practices for filtering, which we use when training and onboarding customers. In addition to the basic templates that come default with the software, these more fleshed-out templates are available upon request. This first blog in the series focuses on germline variant analysis. Rare Pathogenic Variants The… Read more »

Collapse Phased Variants in VarSeq

         September 12, 2024

In a recent blog post, we explored how phased genotypes provide crucial insights by separating variants into distinct haplotypes—groups of alleles inherited together from a single parent. We also discussed how the combined impact of multiple variants within the same gene can significantly differ from their individual effects. However, accurately assessing the joint impact of these in-phase variants is a… Read more »

Our New Pharmacogenomic Tutorial is Hot Off the Press!

         August 1, 2024

Our customers asked for a step-by-step tutorial for navigating a pharmacogenomic (PGx) workflow in VarSeq, and we are happy to have it delivered! Our brand new PGx tutorial can be found on our website, along with our other VarSeq tutorials. Like our other famous tutorials, this one will provide example data, or you may follow along with your own star… Read more »

Where Are My Structural Variant Calls? – Highlighting the Breakends Table

         June 25, 2024

In the last year, we have seen a surge in customers moving to whole genome sequencing. Not only does whole genome sequencing provide unparalleled gene coverage compared to whole exome, but depending on the kind of sequencing, you may expect to see additional file types as well. For example, our partners at PacBio will provide an additional VCF containing copy… Read more »

Couple Carrier Screening Tutorial and Onboarding Training Now Available!

         April 30, 2024

We are pleased to announce new training materials are available for multi-sample workflows in VarSeq! Specifically, we have a New Carrier Screening Tutorial and New Onboarding and Training guides for Carrier Screening Analysis in VarSeq, and Clinical Evaluation and Carrier Status Reporting in VSClinical. This blog gives an overview of what the user can expect to encounter when working through… Read more »

Auto Computation of Coverage Files

         January 18, 2024

The latest VarSeq release offers enhanced control over genome browse visualization computations. These computations, which are responsible for computing and caching coverage files that create the aggregate view of tracks within GenomeBrowse, are now more flexible. Typically, these tracks create files with the “.covtsf” extension and are used for zoomed-out density views of sources like VCFs and BAMs. Managing Automatic… Read more »

Evaluate the use of Evaluation Scripts in your ACMG Workflow!

         September 5, 2023

Recently, we have written a couple of blogs that were talking about the use of Evaluation Scripts in VSClinical workflows, in particular for the AMP workflow. Evaluation scripts were first introduced to VSClinical AMP in VarSeq 2.3.0 and VarSeq 2.4.0 welcomed evaluation scripts to the ACMG Workflow. Evaluation scripts are a nifty way to customize your workflow and say import… Read more »

VarSeq Assessment Catalogs for Beginners

         August 29, 2023

Variant interpretation is a critical aspect of any clinical NGS workflow. VarSeq assessment catalogs are a tool used to save variants and associated variant information for easy tracking and retrieval of completed variant interpretations. As variant interpretations stack up and classifications are saved, storing in assessment catalogs makes it easy to automatically fill in a previous interpretation if the variant… Read more »

Data Viewing with VarSeq: Plotting Tracks!

         June 26, 2023

In recent weeks, GenomeBrowse capabilities have had a sudden resurgence of interest among our customers. To support this, the FAS team wanted to share with you several under-utilized GenomeBrowse plotting tricks. First, let’s cover plotting a BED file for easy track viewing. The first step is launching a GenomeBrowse window by clicking the + button and selecting GenomeBrowse (Figure 1)…. Read more »

Transitioning to Broad-Scale Genomics: From Gene Panels to Whole Genome Sequencing

         May 16, 2023

Explore the evolving landscape of genomic analysis, transitioning from targeted gene panels to whole genome sequencing. A recent trend with our customers has been to expand their workflows from small panel sequencing analyses to larger whole exome and genome sequencing analyses. The decreasing cost of sequencing has made this a rather common request. Although more data allows for a greater… Read more »

ACMG STRIKES BACK

         May 4, 2023

Use the force of evaluation scripts to automate and customize your VSClinical ACMG workflow in VarSeq 2.4.0. VarSeq 2.3.0 came packed with new features! Most notably, VarSeq variant analysis expanded to support the import and annotation of structural variant files, and the AMP cancer workflow in VSClinical gained new functionality with the addition of evaluation scripts which help automate and… Read more »

Unraveling Structural Variants with VarSeq: A Comprehensive Workflow

         April 18, 2023

Unlock the potential of VarSeq for efficient analysis of structural variants, providing robust annotation, filtering, and interpretation of intricate genetic variations. While the analysis of structural variants (SVs) is crucial for understanding the genetic basis of disease, the process of interpreting these variations can be a challenging and complex task. Structural variant callers typically store rearrangements in VCF files, which… Read more »

Maximizing Structural Variant Detection with Soft Clip Visualization

         March 27, 2023

Discover how soft clip visualization can help you identify structural variants in your research and improve the accuracy of your findings. Soft clipping is a common technique in sequence alignment used to remove bases from the ends of reads that do not align with the reference sequence. Removing these bases typically improves alignment accuracy. However, when multiple reads are soft… Read more »

Decoding Complex Fusion Representations: A Deep Dive into VCF Breakend Notation and its Impact on Gene Analysis

         March 14, 2023
Decoding Complex Fusion Representations A Deep Dive into VCF Breakend Notation and its Impact on Gene Analysis Icon

Unlocking the intricacies of fusion representations is crucial for understanding the impact of complex genetic rearrangements on gene function and disease development. In the most recent release of VarSeq, we added support for the import of complex rearrangements from VCF files, which typically encode rearrangements using breakend notation. This powerful notation is capable of describing the full spectrum of structural… Read more »

Creating a BED File from RefSeq: A Comprehensive Guide for Accurate Data Analysis

         February 14, 2023

Our FAS team has received a flurry of inquiries recently, asking how to run coverage statistics on their projects without a pre-defined BED file. We’re here to help! To analyze sample coverage statistics, you’ll need a BAM or CRAM file that displays the read depth coverage for your samples. But don’t worry, even if you don’t have a BED file,… Read more »

A New Comprehensive Template for Somatic Variant Annotation and Filtering in VarSeq

         February 2, 2023
A New Comprehensive Template for Somatic Variant Annotation and Filtering in VarSeq icon

Revolutionize Your Somatic Variant Analysis with Our Cutting-Edge Template for Annotation and Filtering in VarSeq Golden Helix is excited to share our new Comprehensive Cancer Template for somatic variant annotation and filtering, along with the latest version of our software VarSeq 2.3.0! Our latest VarSeq update was specifically focused on getting up to speed with multiple aspects of somatic variant… Read more »