Features
With VSReports, you can easily convert the output of your tertiary analysis into a customized clinical report. After you've filtered down your imported variants, simply select variants to include in the report. You are then one click away from a report that includes:
- Identifiers from dbSNP or ICGC somatic mutation catalogs
- Descriptions of gene function from OMIM
- Pathogenicity based on your past variant assessments or Clinvar
- HGVS variant names
- Exon Numbers
- Sequence Ontology
- Coverage Information
- Variant interpretations provided by the user
- Overall Test interpretation
Full Integration of OMIM
VSReports comes with OMIM, a comprehensive catalog focusing on the relationship between the phenotype and genotype of all known Mendelian disorders and over 15,000 genes. The OMIM annotation source will be deeply integrated into VSReports, and carefully curated at the phenotype, gene and variant level.
Customizable Report Templates
Reports can be branded and styled to match the documents that your lab typically produces. With tight integration to your analysis results, you can also pull in additional annotation sources relevant to the sample being tested. we are happy to work with you to design templates specific to your needs.
Modeled off ACMG Guidelines
VSReports ships with report templates that are modeled off of the ACMG guidelines. Templates for both hereditary and cancer analysis are included free of charge.
Customizable Export Formats
Reports are created as HTML documents which can be exported to a PDF with a single click. Export formats are completely customizable and can be tailored to integrate with other services that use formats like XML as their input.
The following descriptive and filterable data points will be joinable to your imported variants:
- Functional description of genes and phenotypes ready for physicians to orient themselves
- Lists of phenotypes linked to genes with supporting evidence and modes of inheritance of the phenotype (autosomal dominant, etc.)
- Paper references with relevant PubMed and direct URL Links to clinical relevant genetic resources such as testing guidelines, ontology and gene test registries
- Descriptive interpretations for variants curated from published papers with family and disease context
Use Cases
Reporting on Gene Panels
VSReports has the ability to generate clinical-grade reports...
VSReports are fully customizable, containing focused and actionable data. It is easy to differentiate primary findings from secondary findings. VS Reports ships with report templates that are modeled off of the ACMG guidelines, the de-facto gold standard for clinical reporting. There are templates available for a gene panel report and a more complex trio analysis. Our reports can be used for both hereditary and cancer analysis and are included free of charge.
Reporting on Clinical Exomes & Trios
Reports can be branded and styled to match the documents that your lab typically produces...
With tight integration to your analysis results, access to OMIM is bundled with this software. However, you can pull in additional annotation sources relevant to the sample tested leveraging our powerful and flexible data import capabilities. By default, reports are created as HTML documents which can be exported to a PDF with a single click. Export formats are completely customizable and can be tailored to integrate with other services that use formats such as XML as their input.
Case Studies
We know our software will exceed your expectations. But don't just take it from us, see how our customers have benefitted from it.
Dr. Benjamin Darbro
Director, Shivanand R. Patil Cytogenetics and Molecular Laboratory
VarSeq had everything we were looking for with regards to annotation, filtering sources and an actual visual browser within the software itself. VSReports allows us to take it all the way to the report generation. But what really set it apart in retrospect is how intuitive it is.Read Dr. Darbro's Entire Case Study
Dr. Laura Li
Associate Director, Children's Hospital Los Angeles
VarSeq is pretty user-friendly. Also the support team is very helpful. They know the VarSeq software in and out and the tech support has helped me to quickly learn VarSeq.Read Dr. Li's Entire Case Study
Recommended Learning Materials
We have a variety of supplemental learning materials to further educate anyone interested in the industry of our software solutions. Here are some of our recommended materials for you to check out related to VSReports!
eBooks
Check out our free eBooks on a variety of different topics:
Webcasts
Watch this webcast that gives a great overview of our clinical stack!
Other Resources
Explore a clinical workflow in VarSeq or follow along with a tutorial!
VarSeq Viewer:
Download Here
VSReports in Action
Download HereTry VSReports for Free
Did you know we offer complimentary trials of our software? No restricted features, no sample data - you get to try all the features of VSWarehouse with your data and see how it works!
If you are interested in a trial, please fill out the form below, and we will send you the details!
Technical Specifications
GENERAL PURPOSE HARDWARE REQUIREMENTS
4 GB of RAM
Multicore CPU
100GB of space available for annotations and projects
ADVANCED AND WHOLE GENOME WORKFLOW HARDWARE REQUIREMENTS
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
OPERATING SYSTEMS
The following operating systems are supported:
64-bit Windows 7 or later
Linux Ubuntu 14.04 or later (64-bit only)
Linux RHEL 7 or later, or equivalently CentOS 7 or later (64-bit only)
Mac OS X 10.11 or later
SERVER CONFIGURATIONS
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.
PROXY SETTINGS, FIREWALLS AND ANTIVIRUS
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.