ChAS software offers an intuitive and flexible workflow for genetic analysis
The new features of ChAS 4.3 are:
- New Mosaic Segmentation Algorithm
- Additional data types supported in VCF
- APIs to push and pull segment coordinates in and out of ChAS
- Support for multiple input/output folders for Automatic Cel Analysis
- Include QC metrics plus Frag QC from Automatic Cel Analysis in QC history file
- Additional annotation track to complete the OMIM morbidity map
- Skip CN <1 for smoothing and joining (for OncoScan)
ChAS, a leading genetic data analysis software that evolves with your lab
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Chromosome Analysis Suite 4.3 (ChAS 4.3)
- Improve mosaic segmentation in both detection as well as breakpoint accuracy
- Co-visualize NGS and microarray data together
- Access supporting evidence for segment prioritization. Add custom annotations prior to uploading into your personal ChAS database for reference in future sample investigation.
- Choose between two prioritization methods to suit your individual needs
- Load samples from ChAS into the Multi-Sample Viewer (MSV) to visualize cohorts of samples simultaneously. Install the MSV as part of the Reproductive Health Analysis Software.
- Display database contents in a histogram track
- Expand your reporting options with the ability to export to Microsoft Word files, create paragraph-style segment tables, generate automatic report file names, and use a quick export button for all graphs and tables
CytoScan Automated Interpretation and Reporting (AIR) Solution
Streamline genetic data analysis to increase productivity with consistent interpretation and reporting
Franklin by Genoox is an end-to-end research solution for the analysis of genetic data with advanced AI-driven interpretation. With CytoScan AIR, our customers can combine the power of both, ChAS and Franklin, to augment the visualizations of CNV gains, losses, and LOH with key clinical research interpretation information.
- AI-driven data interpretation and reporting—consistent, accurate results available in seconds so researchers can focus on discovery
- Strong evidence support—options for segment prioritization include the most up-to-date American College of Medical Genetics (ACMG) classifications, phenotype matching, literature searches, and historic data
- Customized reporting—intuitive and simple-to-use interface enables easy customization, reporting, evaluation, and sign-off
- Database management and expansion: access to Franklin knowledge base enables users to link evidence with observations and assessments for internal database development and curation
- Relevant insights—community-driven cytogenetics research platform provides more than 350,000 shared classifications of variants and advanced metrics
Featured video
An overview of the ChAS 4.2 and 4.3 features and updates.
ChAS training videos
Compare your current analysis pipeline and see what features you may be missing out on
In addition to the support for ChAS offered from our technical teams, we now offer these convenient on-demand training videos. They are easy to follow, cover a wide range of topics, and are each designed to be viewed in only 20-40 minutes. Whether you’re a seasoned expert looking for a refresher or a potential new user to ChAS, the videos offer helpful training when your schedule allows.
Compare your current CMA software to ChAS by viewing the featured module below. Then access all modules using the button below.
ChAS training modules
- ChAS Software Installation
- Analysis Workflow Overview
- Overview of the ChAS Browser
- CNV and LOH Data Review
- ChAS Database Overview
- CytoRegions and Overlap Map: AED and BED Files
- Sample case complete analysis workflow
- ChAS version 4.2.1 features
Additional software files and sample data sets
Analysis files
ChAS requires sets of analysis files to create and visualize copy number, LOH, and genotyping data files for CytoScan Cytogenetics Suite, OncoScan CNV Plus Assay, and OncoScan CNV Assay arrays.
To download these files into the appropriate ChAS library folder from within the software, use the Help>Update Library and Annotation Files functionality or download them from the Analysis Workflow using Utilities>Download Library Files. Within RHAS you can download them from Preferences>Download Library Files.
Alternatively, to copy the files into your ChAS Library folder manually, download the Analysis Files.zip to the data analysis workstation, extract the zip archive, open the folder containing the files, copy all of the files, and paste them into the ChAS Library, using the instructions in the ChAS User Guide located in the ChAS software zip package.
Download ChAS 4.3
Download RHAS 1.1
ChAS 4.3 Library
CytoScan XON Array Analysis Files hg19.r7 Part 1
CytoScan XON Array Analysis Files hg19.r7 Part 2
CytoScan XON Array Analysis Files hg38.r7 Part 1
CytoScan XON Array Analysis Files hg38.r7 Part 2
CytoScan 750K Array Analysis Files NA33.r9
CytoScan 750K Array Analysis Files NA36.r6
CytoScan HD Array Analysis Files NA33.r9
CytoScan HD Array Analysis Files NA36.r6
CytoScan Optima Array Analysis Files NA33.r9
CytoScan Optima Array Analysis Files NA36.r6
ChAS 4.3 Analysis Files for OncoScan CNV Array hg19 NA33.r8
ChAS 4.3 Analysis Files for OncoScan CNV Array hg38 NA36.r5
ChAS 4.3 Analysis Files for OncoScan CNV Plus Array hg19 NA33.r6
ChAS 4.3 Analysis Files for OncoScan CNV Plus Array hg38 NA36.r5
NetAffx Genomic Annotation Files
Sample data sets
The sample data zip package for the different array types includes data files and a description key document.
CytoScan HD Array
OncoScan CNV Plus Assay
Download ChAS 4.3
For Research Use Only. Not for use in diagnostic procedures.
