Genotyping Console™ Software

Genotyping Console™ (GTC) Software makes primary data analysis easy with simple drop-down menus and visualization tools that help you get to your data quickly and dig deeper for quality checking and biological meaning.

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GTC Software integrates single nucleotide polymorphism (SNP) genotyping, copy number polymorphism (CNP) genotyping, rare copy number variation (CNV) identification, and cytogenetic 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, version 4.1.4 please select the appropriate link below:

Genotyping Console Software 4.1.4 (64-bit) *Posted on 02/19/2013
Genotyping Console Software 4.1.4 (32-bit) *Posted on 02/19/2013

This version is supported on both Windows 7 (both 32-bit and 64-bit) and Windows 2008 Server (64-bit). Please refer to the release notes for information on installation/upgrade requirements and all updates to the software by selecting the appropriate link.

New features

GTC version 4.1.4 includes all features of GTC 4.1.3 and additionally has the following new features and updates:

Ability to export summary calls text file with intensities for performing CNV analysis with data generated using the Axiom® Genotyping Solution.
Ability to export text files required by the SNPolisher™ analysis and visualization package for agrigenomics genotyping data generated using the Axiom® myDesign™ custom genotyping arrays.
Exports data for analysis in PLINK. All probesets in the CHP file that do not exist in the annotation file now have the correct probeset ID associated with them in the exported file. Such probesets that do not have annotation information will get 0s in the exported PLINK file.

Figure 1

Figure 2

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 3

Figure 3 caption: A screenshot of a cluster graph displayed in GTC 4.1.3. 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 4.1.3 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).

GTC Software version 4.1.4 enables:

Automated genotype calling and Copy Number analysis on data generated from:

Axiom™ pre-designed genotyping arrays (human and non-human)
Axiom myDesign™ custom genotyping arrays

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
New call rate metrics calculation methods – Call_rate, hom_rate, and het_rate are calculated using autosomal SNPs only.

Automatic cluster 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
Gender to provide gender information
Inbred samples to control bias against inbreeding

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 such as call rate, FLD, HomFLD, Het Strength Offset, Hom Ratio Offset, Minor Allele count, number of clusters, etc.
Exports *.calls.txt, *.confidences.txt, *.summary.txt, *.report.txt, *.snp-posterior.txt as input for SNPolisher™ for advanced analysis and to categorize the SNPs for easy visualization. SNPolisher™ is an R-based package that uses the analysis results from agrigenomics genotyping arrays to categorize SNPs into >5 categories eg. polymorphic SNP clusters, off-target variant clusters and no-minor homozygous clusters.
Capability to export *.summary.txt file text file with signal intensities for performing CNV analysis with data generated using the Axiom® Genotyping Solution.

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 new 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
Hg19 support:

Support Hg19 version of Canary algorithm
Support Hg19 version of browser annotation files for the Genome-Wide Human SNP Array 6.0, Human Mapping 500K Array Set, and Human Mapping 100K Array Set

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.