Simple, fast and repeatable variant analysis software for gene panels, exomes and whole genomes.


VarSeq is an intuitive, integrated software solution for tertiary analysis. With VarSeq you can automate your workflows and analyze variants for gene panels, exomes and whole genomes.

Intuitive & Repeatable Workflows

VarSeq® software provides a powerful filtering and annotation engine to sift through large variant data sets. Using a chain of filters, you can quickly narrow your list of variants down to those that are most likely to be of interest. After determining the parameters that work well for your analysis, you can save the state of your filters so that you can easily apply the same analysis to another dataset. The same automated workflow can be used for each batch of samples, making VarSeq ideally suited to high-throughput environments. Real-time filtering gives you the power to quickly prototype and tune analysis workflows to the specific gene panels that your lab uses. Once the appropriate set of filters have been found, the workflow can be saved and applied to future sequencing outputs without having to re-enter any parameters.

Industry leading annotation sources

After data import, annotations are automatically applied based upon your pre-configured settings. Additional annotations can then be added at any time during the analysis process. The Golden Helix ® team curates a wide selection of public databases and updates these datasets on a quarterly basis. The specific annotations used in your analysis are stored locally with your data and are never changed without your explicit request. This ensures that your analysis is performed on a stable dataset and your results are reproducible and available in the future.

Coverage Statistics

VarSeq provides coverage metrics in two forms. First, each variant displays data about the region in which it resides. This binding allows variants from suspect regions to be flagged or filtered out, which can help to prevent false positives. Second, each region in the BED file can be examined. This mode of analysis ensures that all the targeted regions were sequenced, which is crucial to preventing false negatives.

Clinical grade variant annotations

Included in VarSeq is functionality similar to SnpEff or Variant Effect Predictor. Each variant is mapped to all overlapping transcripts and information about the region where it is located (exon, intron, intergenic, etc.), sequence ontology (frame shift, synonymous, etc.), and HGVS notation (g dot, c dot, and p dot) is provided. You can chose to filter against the highest-impact annotation for each variant or the entire set of variant-transcript interactions.


Since GenomeBrowse is built into VarSeq, it is easy to verify coverage across your amplicons. Simply add your BAM and BED files to your project and inspect the pileups directly. GenomeBrowse provides the context you need to have confidence that your upstream sequencing pipeline is working correctly.

No learning curve

Import your data, select a workflow and start exploring. It is that simple! No uploading data. No complicated parameter selection. No difficult file conversions. VarSeq distills the analysis process down to its very essence and removes all roadblocks that get in the way of getting work done.

Use Cases

Cancer Diagnostics

Make breakthroughs in cancer diagnostics with supported gene panel testing and whole exome and genome analysis.

  • Support for Cancer Gene Panels: VarSeq includes the specialized features needed for cancer workflows. Allelic ratios are automatically calculated to detect somatic mutations at low tumor fractions. Additionally, variants can be annotated precisely against COSMIC, fully utilizing the many somatic mutation annotations present in the database. Finally, variant blacklists can be imported to filter variants that your lab has found to be inaccurate or not actionable.
  • Whole Exome and Whole Genome Analysis: VarSeq enables cutting edge cancer analysis by easily supporting whole exome and genome sized datasets.
  • Tumor/Normal Workflows: VarSeq provides complete support for Tumor Normal workflows. Samples can be imported as matched pairs, allowing germ line variants to be filtered out in a single step. Multiple paired samples can be imported in a single project enabling fast and accurate analysis in settings where reproducibility is critical.
  • COSMIC: Included in VarSeq is the Catalogue of Somatic Mutations in Cancer or COSMIC. COSMIC is a population catalog containing somatic mutations related to human cancer. The release of COSMIC V71 integrated The Cancer Genome Atlas, making it the most compressive catalog of somatic mutations in history. VarSeq also provides the gene level annotations with relevant summary and curated oncology details provided by COSMIC. COSMIC breaks out each sample-variant pair into a record, and VarSeq provides the fields in COSMIC with relevant hyperlinks and formatting to enable easy filtering. As with all of our public annotation libraries, COSMIC is updated regularly, providing you with the most recent and relevant data.
  • MedGenome's OncoMd Integration: VarSeq offers the ability to access OncoMD's comprehensive knowledge base of over 2.3 million annotated cancer variants captured from peer-reviewed scientific publications by a team of biomedical curators. After filtering variants of interest in VarSeq, you can quickly prioritize actionable variants using OncoMD and make clinical decisions based on the sensitivity of variants to approved drugs and enrollment to open clinical trials. Inheritance based filters include: autosomal dominant, autosomal recessive, de novo, compound heterozygous and more.

Hereditary Testing & Diagnosis

Helps clinical testing laboratories complete the time-critical and patient-centric workflows for gene testing and rare disease diagnosis

  • Comprehensive Workflows: The VarSeq clinical stack supports all of the steps necessary to provide clinical genetic tests from the raw VCF variants to the signed out clinical report. VarSeq's flexibility allows you to customize workflows to the individual gene panel or exome test.
  • Supported Genetics Tests Include: Diagnostic testing used to identify the presence or absence of causal genetic variations for specific disease , predictive and pre-symptomatic genetics tests designed to identify hereditary gene changes that can increase the lifetime risk of developing diseases, and Newborn Screening used to test babies soon after birth to identify highly penetrant variants for certain diseases known to cause problems with health and development.
  • Rare Disease Diagnosis: VarSeq includes first-class support for the more complex workflows associated with discovering the causal variants of rare disease. This includes using related samples in trios and quad analysis, algorithms that detect inheritance patterns of variants, ranking of rare patheogenic variants by their relevance to the phenotype terms provided by differential diagnositics and the integration of the public and premium annotations sources.


Enables filtering based on inheritence patterns, affection status, and arbitrary sample groupings.

  • Phenotype Based Gene Ranking: Variants can be prioritized by examining how closely the mutated gene is related to the patient's phenotype. By examining biomedical ontologies that link diseases with genes, the algorithm can rank genes according to the proband's phenotype. These generated rankings can be combined with traditional filtering techniques to quickly surface candidate variants.
  • Powerful Variant Annotation: Included in VarSeq is functionality similar to SnpEff or Variant Effect Predictor. Each variant is mapped to all overlapping transcripts and information about the region where it is located (exon, intron, intergenic, etc.), sequence ontology (frame shift, synonymous, etc.), and HGVS notation (g dot, c dot, and p dot) is provided. Additional statistics, such as distance from coding start, distance from exon boundary, and the number of codons changed make it easy to examine specific classes of variants.
  • Inheritance and Affection Status Based Filtering: VarSeq includes first-class support for workflows that use pedigree, affection status, or custom groupings to define filter criteria. Prebuilt filters are available for most common inheritance patterns. Custom filters can be easily created using family information. Additionally, affection status alone can be used to construct useful segregation analysis of complex family pedigrees to find candidate regions and variants.

Trio Analysis

VarSeq provides the ability check for all modes of inheritance in parallel leveraging proven and tested parameter settings for complete data analysis, filtering and interpretation workflow.

In combination with our PhoRank algorithm, we can effectively zero in on the most relevant variants and sort them by relevance in conjunction with the phenotype.

Case Studies

We know our software will exceed your expectations. But don't just take it from us, see what our customers have benefitted from it.

Recommended Learning Materials

We have a variety of supplemental learning materials that are an excellent resource for anyone interested in the industry or our software solutions. Here are some of our recommended materials for you to check out related to VarSeq!


Check out our free eBooks on a variety of different topics:

Other Resources

Explore a clinical workflow in the VarSeq or follow along with a tutorial!

VarSeq Viewer:
Download Here

Introduction to VarSeq:
Download Here


Request a free trial of VarSeq!

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Technical Specifications


4 GB of RAM

Multicore CPU

100GB of space available for annotations and projects


If you are working with whole exomes or genomes, especially if or hundreds to thousands of samples, we suggest a high-memory configuration and plenty of storage capacity:

16GB+ of RAM (32GB for Servers)

8+ CPU Cores

1TB of space available for annotations and projects


The following operating systems are supported:

64-bit Windows 7 or later (32-bit also supported, but not recommended)

Linux Ubuntu 14.04 or later (64-bit only)

Linux RHEL 6 or later, or equivalently CentOS 6 or later (64-bit only)

Mac OS X 10.9 or later


With a server license, you can install your Golden Helix software solution on a server with multi-user access and shared resources. You can launch any number of instances of the software on the same host, and are only limited by the natural CPU, Memory and Disk resources of the server.

For Windows, you would need to use ability for multi-user Remote Desktop only available on Windows Server. We support Windows Server 2008 or newer.

On Linux, clients can log in from any operating system using SSH and open the Golden Helix software using X11-tunneling to interact with the software. On windows, we suggest a solution like MobaXterm that provides a all-in-one SSH client and X11 server to enable easy logging in, file transfer and opening of remote GUI applications.


Golden Helix VarSeq and SVS can be configured to access the internet through a SOCKS5 or HTTP/HTTPS Tunneling Proxy. Go to Tools -> Proxy Settings… to configure.

The software only needs to make outgoing connections on standard HTTP/HTTPS ports and protocols. If a local firewall is installed that prevents these types of outgoing connections (this is very uncommon), firewall rules will need to be created to whitelist the software.

Note we have run into numerous issues where aggressive anti-virus programs prevent the product from performing normal operations such as opening files and logging in. You may need to whitelist Golden Helix executables or disable these tools to perform your analytics.