Genotyping Console (GTC) Software integrates single nucleotide polymorphism (SNP) genotyping, indel detection, and copy number variation (CNV) analyses into one application. It generates genotyping calls, copy number calls for CNV regions and individual probe sets, loss of heterozygosity (LOH) data, cluster plots (Figure 1 and Figure 3), and quality control metrics. GTC Software is also used for analysis of data from agrigenomics arrays for diploid and polyploid species.

Download information and instructions

To obtain the latest version of Genotyping Console Software, version 4.2, please select the link below:

Genotyping Console Software 4.2 (64-bit Windows 7 and Windows 8.1) *Posted on 04/7/2014

The latest version of Genotyping Console Software is supported on Windows 7 (64-bit) and Windows 8.1. Please refer to the release notes for information on installation/upgrade requirements and all updates to the software by selecting the appropriate link.

For use on 32-bit and/or Windows XP systems, please select the Genotyping Console Software 4.1.4 link below:

Genotyping Console Software 4.1.4 (32-bit Windows XP only) *Posted on 02/19/2013

New features

GTC version 4.2 includes all features of GTC 4.1.4 and additionally has the following new features and updates:

  • Ability to change genotype calls for individuals or groups of samples using a lasso
  • Simplified one-click export of summary calls text file with intensities for performing CNV analysis with data generated using the Axiom Genotyping Solution. CNV analysis can be completed in third-party software such as Nexus Copy Number™ Software from BioDiscovery or PennCNV, a free software tool for CNV detection from SNP genotyping arrays

GTC Software version 4.2 enables:

  • Exporting text files required by the SNPolisher™ analysis and visualization package for agrigenomics genotyping data generated using the Axiom myDesign™ Custom Genotyping Arrays. SNPolisher is an R-based package that uses the analysis results from agrigenomics genotyping arrays to categorize SNPs into >5 categories (e.g., polymorphic SNP clusters, off-target variant clusters, and no-minor homozygous clusters)
  • Exporting of data for analysis in PLINK. All probe sets in the CHP file that do not exist in the annotation file now have the correct probe set ID associated with them in the exported file
Figure 1 Figure 1: Graphical representation of sample and processing information in the cluster plot

Data are displayed in tabular and graphic formats, allowing you to easily share your results with others. Flexible SNP filtering (Figure 2) and export tools are included to enable downstream statistical analysis.

Figure 2 Figure 2: Flexible SNP filtering capabilities
Figure 3 Figure 3: Cluster graph displayed in GTC 4.1

Figure 3: A screenshot of a cluster graph displayed in GTC 4.2. Both the SNP cluster priors (dashed-line cluster boundaries as defined by Affymetrix training data) and SNP cluster posteriors (solid-line cluster boundaries as defined by experimental data combining information from priors) are shown. Additionally, this screenshot illustrates the lasso functionality available in GTC 4.2 cluster graph, which allows you to manually capture samples of interest (from the cluster graph) for identification in the sample table (table displayed below the cluster graph) or for changing the genotype calls.

  • Automated genotype calling, clustering and copy number analysis on data generated from Axiom Genotyping Arrays (human and non-human)
  • Automatic clustering and genotype calling of data from polyploid and diploid genomes. The software has the capability to use additional information about the samples to improve genotyping performance. This includes:
    • Hints to train difficult SNPs with known reference genotype data
    • Capability to genotype as few as 20 samples using SNP specific priors
    • Gender to provide gender information
    • Inbred samples to control bias against inbreeding
  • GTC Software provides the ability to customize genotyping analysis through the following options:
    • Select a subset of SNPs to analyze for genotyping
    • Create and select model files; use customized models file for future genotyping
    • Call rate metrics calculation methods – Call_rate, hom_rate, and het_rate are calculated using autosomal SNPs only
  • An enhanced implementation of the two-stage genotyping workflow that provides text files for the advanced analysis workflow using R. These include:
    • Exports *.calls.txt, as input to R codes to generate SNP metrics
  • Enhanced graphs and other GUI tools:
    • Quickly identify features of interest in your data set with scatter plots, line graphs, and heat map graphs
    • View prior/posterior ellipses in the cluster graph for most arrays (Figure 3)
    • A sample table display for displaying information about sample attributes
    • A lasso function to select data points in the cluster plot and identify selected samples in the sample table displayed below the cluster plot (Figure 3)
    • Interaction between the sample table and cluster graph enable you to dynamically identify samples of interest
  • Calculate copy number state for use in statistical association analyses and high-resolution CNP mapping

GTC Software gives you the flexibility to analyze data from a range of Affymetrix arrays while providing data analysis continuity. The software seamlessly integrates with third-party software packages.

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