Bioinformatic Support

Evaluation Script Adding Variants to Catalog

Apr 23, 2024

Variant curation is one of the most important aspects of a next-generation sequencing workflow. The routine application of previously rendered interpretations, paired with the ability to take into account evolving knowledge bases, allows clinical practices to rapidly and accurately provide life-saving results to patients. Hence, assessment catalogs, versatile databases that…

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Computed Fields in VarSeq: The Ultimate Customization Tool

Apr 2, 2024

Bioinformatic freedom is core to the user experience with Golden Helix software, a topic with which you will be well-versed if you’ve kept up on our recent blogs. We are constantly endeavoring to provide our users with powerful tools to tackle complex and impactful next-generation sequencing (NGS) workflows while maintaining…

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Five Ways to Optimize Workflows with VarSeq

Mar 7, 2024

There are many ways to optimize an individual workflow, from increasing the granularity of a filter chain to automating certain multi-stepped tasks. Although the best way to optimize an individual workflow is to book a session with our FAS team to talk about your unique use case, we wanted to…

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Managing Gene Preferences and Preferred Transcripts in VarSeq

Jan 16, 2024

There are several contextual factors to consider when analyzing genomic data for NGS analyses. A variant may have divergent impacts depending on which transcript of the gene is being considered, or the impact of a variant could be weighed more or less heavily depending on the disease context. Evidently, the…

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Evaluating DeepMind’s AlphaMissense Classifier

Oct 20, 2023

Last month, the researchers at Google DeepMind announced the release of AlphaMissense, a new missense prediction algorithm that leverages the protein structure prediction model AlphaFold to distinguish between benign and pathogenic missense variants (Cheng et al., 2023).  AlphaFold is a model for the prediction of protein structures from amino acid…

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Interpreting Fusions Variants in VCFs: A Handy Tool

Aug 22, 2023

When interpreting fusions in their VCF format, it is not easy immediately grasp which side of the positions are adjacent in the resulting fusion. When interpreting and troubleshooting fusion variants, I usually find myself reaching for the VCF spec. If you, like me, are looking to speed up this process…

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Using Text Manifests to Load in Sample Patient Information

Aug 3, 2023

The ability to import patient-level information into VarSeq and VSClinical can not only save time while evaluating a sample but can be a critical step in automating project creation through VSPipeline. Here we will review how to construct a basic text manifest and how to apply that manifest to a…

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Importing External Assessment Catalogs for use in VSClinical ACMG and VSClinical AMP

Jul 13, 2023

When doing clinical variant analysis, it is often essential to keep track of the variants that are encountered in each sample, their pathogenic or oncogenic classifications, which individual created or saved an interpretation, and when. For this purpose, VarSeq prompts VSClinical users to create default assessment catalogs in which to…

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New Dog, Old Tricks: How to Bring Existing Variant Catalogs into VarSeq

May 15, 2023

Learn how VarSeq revolutionizes NGS workflows by enabling the integration of comprehensive internal databases, allowing bioinformaticians to create custom pipelines and maximize data analysis efficiency. Are you a current (or future) VarSeq user with a perfect, comprehensive, internal database you simply can’t part with and can’t replicate? Do you dream…

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VarSeq Customization and Automation with VSCode

Mar 9, 2023

Enhancing VarSeq Customization and Automation with Visual Studio Code: A Guide to Evaluation and Reporting Scripting Are you as excited as we are about the new automation and customization features we’ve been rolling out with VarSeq’s most recent release, VarSeq 2.3.0? Do your eyes light up at the prospect of…

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Exploring the CRAM File Format in VarSeq 2.3.0

Jan 17, 2023

Unlocking the Potential of CRAM Files: The New VarSeq 2.3.0 Release for Enhanced Plotting, Coverage Analysis, and CNV Detection The CRAM (Compressed Reference-oriented Alignment Map) file format was conceived in 2011 as a more space-efficient way to store alignment data. It saves space over the previous standard BAM (Binary Alignment…

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4 Essential Support Resources for Golden Helix Software Users

Jan 5, 2023

Golden Helix provides extensive resources to help our users who are just getting started and address any issues they may encounter as they become more familiar with our software. Our resources are constantly updated and are tailored to the needs of our users. If you’re facing a problem, it’s likely…

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Using rsID lookup in a VarSeq Workflow

Oct 4, 2022

There are many reasons a user may wish to focus in on specific variants as part of variant annotation and filtration workflow. You may be looking for the occurrence of specific SNPs in a cohort or perhaps looking for variants known to be associated with specific forms of cancer. For…

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Streamlining Variant Analysis for Large Genetic Cohorts: Part 1

Sep 27, 2022

Large genetic cohorts require substantial effort to analyze. Genetic researchers are increasingly turning to whole exome and whole genome sequencing analyses for their clinical diagnostics and research. However, with that approach comes the challenge of making sense of these massive datasets. This is especially challenging when looking for tools that…

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Using ACMG Secondary Findings v3.0 List in VarSeq and VSClinical

Dec 21, 2021

As the number of genes on a gene panel increases, there is the possibility of picking up variants of medical significance that are not related to the primary indication for the test. Especially with large gene panels, exomes, and genomes, it is medically and ethically important to report variants that…

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Consideration when using CADD in your NGS Workflow

Dec 15, 2021

VarSeq serves as a streamlined approach to handle the rare variant analysis typically carried out for your next-generation sequencing data. Our team at Golden Helix seeks to simplify this process by automating the curation of staple databases needed for filtering and evaluation of clinically relevant variants. The goal we seek…

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Alternate Allele Frequency and VCF File Format

Dec 7, 2021

VCF file format comes with a lot of interesting quality assurance and statistics fields that can be used for filtering in VarSeq. Open your files in a text editor to see all the fields that are available in your files, each field will have a header line with a description…

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Selecting Clinically Relevant Transcripts in VarSeq

Jun 28, 2021

One of the many tricks of encoding so much functionality into so little space in eukaryotic genomes is the ability to produce multiple distinct mRNAs (transcripts) from a single gene. While one transcript is often the dominant one for a given tissue or cell type, there are, of course, exceptions…

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A Simple Guide to Curating Genome Assemblies

Jun 8, 2021

A common feature request from Golden Helix customers is to curate and make available genome assemblies for different plant and animal species. These requests commonly come from SVS users as many research projects are being carried out, and having the genome assembly available for analysis is essential. That being said,…

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Importing CNVs using VSPipeline

Jun 2, 2021

VSPipeline is a command-line interface that will provide high throughput environments the ability to tap the full power of VarSeq’s algorithms and flexible project template system from any command-line context, including the existing bioinformatics pipeline. This feature is a great resource for analyzing large sample volumes as it automates importing…

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