ChAS software offers an intuitive and flexible workflow for genetic analysis

Chromosome Analysis Suite (ChAS) software was developed with input from leading experts and is customized for copy number and cytogenetics research analysis and reporting. ChAS enables you to view and summarize chromosomal aberrations across the genome. Chromosomal aberrations may include copy number gain or loss, mosaicism, or loss/absence of heterozygosity (LOH/AOH).

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)
Chromosome Analysis Suite (ChAS) software

ChAS, a leading genetic data analysis software that evolves with your lab

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Chromosome Analysis Suite 4.3 (ChAS 4.3)

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

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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.

Access all modules

ChAS training modules

  1. ChAS Software Installation 
  2. Analysis Workflow Overview
  3. Overview of the ChAS Browser 
  4. CNV and LOH Data Review 
  5. ChAS Database Overview
  6. CytoRegions and Overlap Map: AED and BED Files 
  7. Sample case complete analysis workflow
  8. 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 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.

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.