VarSeq Suite

VarSeq Suite: Clinical Genomics Software

Run clinical variant analysis, ACMG/AMP interpretation, and report sign-out on one platform. Automate your NGS workflows from raw VCF to a signed clinical report backed by an ISO 13485-certified quality management system.

Request EvaluationSee How It Works
ISO 13485 Certified QMS
CE Marked (IVDR)

Clinical genomics software turns sequencer output into a signed clinical report. It runs the steps a diagnostic lab needs between VCF and sign-out: annotation, filtering, ACMG/AMP classification, and reporting.

Panels, exomes, and genomes all land in the same workflow. A unified variant analysis software lets your lab keep one filter chain, one classification rubric, and one report template across every assay, while staying current with ACMG and AMP guidelines.

The VarSeq Suite is Golden Helix's NGS interpretation platform for tertiary analysis. Curated monthly annotations, real-time filter chains, and guided ACMG/AMP workflows give clinical scientists the inputs they need to classify a variant and sign a report in one session.

See how it works

What Is Clinical Genomics Software?

Clinical genomics software handles human genetic data inside a regulated lab. Three things matter once a result leaves the bench and heads toward a patient chart:

  • Reproducibility: Audit and re-run any analysis to identical results months or years later.
  • Curated Evidence: Integrating population frequencies, functional predictions, and literature into a single view.
  • Regulatory Alignment: ISO 13485-Certified QMS; VarSeq Dx is CE marked under IVDR 2017/746 for in vitro diagnostic use in the European Economic Area. Designed to support CAP and CLIA requirements.

Why Clinical Genomics Software Matters

A clinical NGS platform earns its keep by raising diagnostic yield, cutting turnaround time, and keeping operational risk low enough to pass audit.

  • Operational Scale: Automate the filtering of thousands of variants to find the few that truly matter for the patient.
  • Patient Safety: Reduce human error through standardized workflows and automated evidence gathering.
  • Knowledge Retention: Build a lab-specific knowledgebase of variant assessments that grows with every sample processed.

What to Look for in Clinical Variant Analysis Software

Automation Capabilities

The software should support full automation from FASTQ/VCF import to report generation without losing clinical oversight.

Annotation Quality

Look for platforms that offer monthly curated updates to ClinVar, gnomAD, and other essential genomic catalogs.

Flexible Deployment

Maintain full data sovereignty with on-premises, private cloud, or air-gapped deployment options that you control.

Regulatory & Quality Framework

Verify that the vendor has an ISO 13485-certified quality management system and supports the needs of CAP/CLIA validated laboratories.

Full Spectrum Variants

A single platform should handle SNVs, Indels, CNVs, SVs, and pharmacogenomic star alleles across panels to genomes.

Audit Readiness

Built-in versioning and state saving ensure every clinical decision is tracked and reproducible for years to come.

How VarSeq Suite Supports Clinical Genomics

One toolset covers the steps that usually require three or four. Your scientists annotate, filter, classify, and report inside VarSeq, with the same audit trail running through each step.

ISO 13485 Quality

Golden Helix develops VarSeq under an ISO 13485-certified quality management system. VarSeq Dx is CE marked under IVDR 2017/746 for in vitro diagnostic use. Installation verification and tiered proficiency certification keep deployments clinically ready.

Curated Annotations

Each VarSeq install pulls monthly-curated data from ClinVar, gnomAD, and premium sources including Golden Helix CancerKB™, OMIM, LOVD, and Genomenon.

Automated Workflows

Run VSPipeline to take a sample from sequencer output to clinical report without an analyst clicking through the pipeline by hand.

Comprehensive Capabilities
Annotation
Transcript Impact
Annotation
Splice Site Prediction
Algorithm
Cohort Allele Frequencies
Algorithm
PGx Star Allele Caller
Automation
ACMG Auto Classifier
Automation
Oncogenicity Classifier
Analysis
Phenotype Gene Ranking
Analysis
Disorder Gene Panels
Inheritance
Compound Het
Inheritance
de Novo Analysis

The VarSeq Clinical Analysis Workflow

1

Import & Annotate

Load VCF or FASTQ data. VarSeq enriches each variant with the current month's clinical and population annotations on import.

2

Filter & Prioritize

Apply real-time filter chains with nested logic and phenotype-driven prioritization. The clinically relevant variants surface in seconds, not minutes.

3

Interpret & Classify

Work through ACMG/AMP criteria in VSClinical with evidence gathered and scored alongside each rule, so the final classification carries its rationale with it.

4

Report & Sign-out

Generate a structured clinical report and archive every assessment in VSWarehouse, so the next sample with the same variant inherits your prior call.

A Unified Platform for All Clinical Needs

Explore the core capabilities of the VarSeq Suite, from specialized variant analysis to end-to-end automation.

Variant Analysis

Real-time filter chains with nested logic, curated annotations, and phenotype-driven prioritization.

Clinical Interpretation

Guided ACMG/AMP classification with automated criteria recommendation.

CNV & Structural Variants

Full-spectrum CNV, breakend, fusion, and tandem repeat detection and reporting.

Pharmacogenomics

PGx star allele calling and diplotype determination with CPIC guidelines.

Workflow Automation

Scale your laboratory with high-throughput VSPipeline automation.

VSWarehouse

Enterprise data management and longitudinal tracking of variant assessments.

Broad Spectrum Clinical Applications

Precision Oncology

Automate the interpretation of somatic variants using AMP guidelines, integrating therapy matching and clinical trial search.

Explore Oncology Solutions

Rare Disease Diagnosis

Support for trio and extended family analysis with de novo, compound het, and phenotype-based variant prioritization.

Explore Germline Solutions

Carrier Screening

Partner-paired workflows for reproductive risk analysis, supporting autosomal and X-linked recessive disorder screening.

Explore Prenatal Solutions

Trusted in clinical labs worldwide

Over 400 institutions run Golden Helix software, from small diagnostic labs to national genome centers.

  • ISO 13485:2016: Golden Helix maintains ISO 13485:2016 certification for the design and development of medical device software.
  • On-Premises Security: Run air-gapped or in your private cloud, so patient data stays inside your infrastructure.
  • Global Adoption: Trusted for routine diagnostics in over 50 countries across germline and somatic testing.

Supporting Platform Capabilities

Sentieon
Secondary Analysis & Alignment
Genomenon Mastermind
Curated Evidence Integration
Premium Annotations
Golden Helix CancerKB™, OMIM, LOVD & CADD
Flexible Deployment
Cloud, On-Premise & Air-Gapped
Security & Compliance
ISO 13485 & CAP/CLIA Readiness
Integrations & API
Connect with LIMS, EMR & EHR

Frequently Asked Questions

Is VarSeq suitable for whole-exome and whole-genome analysis?

Yes. VarSeq handles WES and WGS sample sizes with high-performance filtering and phenotype-driven prioritization, surfacing clinically relevant variants without bogging down on millions of rows.

How often are the annotation sources updated?

Golden Helix provides monthly curated updates to all major annotation sources, including ClinVar, gnomAD, OMIM, on both GRCh37 and GRCh38, ensuring your analysis is based on the most current data.

Does VarSeq support both germline and somatic workflows?

Yes. VarSeq runs dedicated workflows and guided clinical interpretation for germline (ACMG) and somatic (AMP) variants on the same platform, sharing one filter library and one report template across both.

Does VarSeq support both short-read and long-read sequencing data?

Yes. VarSeq natively supports short-read data from Illumina and long-read data from PacBio and Oxford Nanopore. Through our partnership with PacBio, VarSeq delivers optimized workflows for long-read variant calling, structural variant detection, and tandem repeat analysis, helping resolve complex genomic regions that short-read platforms miss.

What types of studies and sample configurations does VarSeq support?

VarSeq is built to handle a wide range of study designs. Analyze single proband samples, parent-child trios, and extended pedigrees for rare disease diagnosis. Run carrier screening with partner-paired workflows. Perform cohort studies with population-level filtering and shared variant assessment. Whether you're running a targeted gene panel, clinical exome, or whole genome, VarSeq adapts to your sample configuration.

Does VarSeq support both GRCh37 and GRCh38?

Yes. VarSeq provides equal support for both GRCh37 and GRCh38, including updated reference sequences, gene models, and the full suite of clinical annotations on each assembly. Where possible, annotations are natively aligned to each genome build; when native alignments are not available, we use liftover to ensure every clinical annotation is accessible on both assemblies. VarSeq also allows you to liftover your variants on import, so you can annotate older GRCh37 data against the latest GRCh38 resources.

Can VarSeq be deployed on-premises?

Yes. VarSeq is designed to run on your local infrastructure or private cloud, providing complete data sovereignty. We also support fully air-gapped environments for maximum security.

VarSeq Insights & Webcasts

Learn how to optimize your clinical NGS workflows with expert-led webinars and articles.

Featured Articles

All VarSeq Articles →

On-Demand Webcasts

View All Platform Webcasts

See VarSeq run on your data

Talk to our clinical scientists about deployment, licensing, and what a VarSeq evaluation looks like for your panel, exome, or genome workflow.

Request Evaluation
View Licensing & Pricing→
Predictable Scaling
Data Sovereignty
ISO 13485 Certified QMS