VarSeq Software

Simple, fast, and repeatable variant discovery and interpretation workflows for gene panels, whole exomes, and whole genomes.

Cancer Diagnostics

VarSeq enables breakthrough discoveries in cancer diagnostics by supporting gene panel testing and whole exome and genome analysis.


Gene Testing & Rare Disease Diagnosis

Complete the time-critical and patient-centric workflows for gene testing and rare disease diagnosis.


Copy Number Variant Calling

Directly call CNV's in target regions and avoid the cost and turn-around time of additional CMA or MLPA testing.



Accelerate the discovery of rare, high-impact variants in family-based analysis, case-control studies and single sample workflows using exome or whole genome data.


Clinical Reporting

Convert the output of your tertiary analysis into a customized clinical report in one click.


Automating Your Clinical Pipeline

VarSeq's command line runner works with your existing bioinformatics pipeline to leverage VarSeq's powerful and flexible workflows.


Genetic Data Warehouse

A scalable, multi-project warehouse for NGS variant call sets, clinical reports and catalogs of variant assessments, allowing labs to leverage volumes of data.


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 annotation curation process ensures that the data is of high quality and will work with your imported variants. While the current versions of these databases are always available, past versions are also accessible. 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.

Available Annotations:

  • ClinVar
  • SIFT and PolyPhen
  • Ensembl Genes
  • GENCODE Genes
  • OMIM
  • dbSNP
  • RefSeq Genes
  • NHLBI 6500 Exomes
  • Client Specific Annotations

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.

Multiple Sample Support

VarSeq can import any number of samples at one time. Using the VCF files already produced by your pipeline, all the variants found in each sample are imported into the program. Each sample is automatically annotated according to any of the pre-configured workflows that you have created. The variants can then be reviewed in aggregate or by sample.

Track Variants Across Projects

Assess the impact of variants and add them to a personal variant database. Use the variants in your database as an annotation source to reference your previous assessments in future samples. Easily build up custom white or black lists for variants to be sure that important mutations are always highlighted. Multiple database back-ends are supported to accommodate any size lab and enable access for all lab members.

Control Your Data & the Annotation Library

VarSeq allows you to maintain control of your data. Your data remains on your computer so you don't have to worry about cloud security, long term storage, or network access. All annotations, algorithms, and workflows are stored on your computer, giving you confidence that your results are consistent from one sample to another.

Additionally, your results are driven not only by your set of input variants, but also by the data sources you use to annotate those variants. Modifying either can cause your findings to change. To keep the ground from shifting underneath your analysis, Golden Helix is committed to providing access to past annotation databases as well as curating the latest annotations as they become available by data providers. Furthermore, the annotations used are stored in your project so there is never a question of whether a newer version of a database has changed your previous results. Take control of your data and never be left wondering again.

Visualization Provides Confidence

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.

Coverage Statistics

Coverage analysis is an industry best practice for analyzing NGS data in the clinic. It informs the clinician that a particular region of interest is adequately covered by the sequencing process. Consequently, this statistic ensures that the data being analyzed is of high enough quality to support the test results being returned to the physician. Coverage analysis confirms that called variants are in fact real. It also ensures no variants went undetected in tested regions due to an inadequate number of reads.

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.

Statistics generated:

  • Average depth of coverage
  • Minimum read depth
  • Maximum read depth
  • Percent of bases in a region meeting different coverage thresholds

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.

VarSeq Clincal Suite

Related Resources

Case Study - King Abdulaziz Medical City
Dr. Majid Alfadhel

Dr. Alfadhel and Dr. Alfares are diagnosing Rare diseases at King Abdulaziz Medical City

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Webcast - Two Clinical Workflows

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Blog Post - Cadd scores
Rank & filter in harmony!
CADD Score

Rule-based filtering and classification mechanisms or rank-based prioritization through all-encompassing “pathogenicity” scores?

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free download - Precision Medicine eBook
Download the Precision Medicine eBook

Precision Medicine

by Dr. Andreas Scherer

Download the eBook »

VarSeq ® Software is intended for Investigational Use Only. The performance characteristics of this product have not been established.