Genotyping Console™ (GTC) Software is the first commercially available software that integrates SNP genotyping, copy number polymorphism (CNP) genotyping, and rare copy number variation (CNV) identification in one data analysis application. The latest version of GTC provides proven tools for genotyping and cytogenetic analysis as well as cutting-edge tools for CNP genotyping.
GTC makes data analysis easy. You can view results in chromosomal and whole-genome contexts with the integrated Genotyping Console Browser and use our simple drop-down menus and visualization tools to access your data quickly, perform quality checks, and explore biological relevance.
This section of the Affymetrix Learning Center provides training on the following new features as well as recently added improvements. Wherever applicable, this training refers to previous Genotyping Console trainings so you can fully leverage the features and benefits.
New features and improvements include:
- New copy number polymorphism (CNP) genotyping algorithm (Canary) to bridge CNP genotyping and classical SNP genotyping analysis within one association study on the SNP Array 6.0 platform
- GC waviness correction algorithm to reduce false positive results and provide more precise segmentation reporting
- High-resolution validated CNP map (Broad Map) included
- Heat map browser for visualizing CN and CNV results - also supports custom map for visualizing and detecting novel CNP regions outside of those identified by the Broad Map
- Enhanced Segment Reporting Tool to support custom map
- Revised MAPD calculation with new threshold recommendation
- Updated SNP Array 6.0 copy number algorithm, previously only available in Affymetrix Power Tools (command line)
- Improved SNP genotyping algorithm (Birdseed) with built-in quality control metric (cQC)
Related Content
Introduction (15:00)
Live Demo: CNV analysis and results visualizations, part 1 (16:00)
Live Demo: Results visualizations, part 2 (12:00)
Live Demo: Segment Reporting Tool enhancements (15:00)