SNPEVG: a graphical tool for GWAS graphing with mouse clicks
© Wang et al.; licensee BioMed Central Ltd. 2012
Received: 11 July 2012
Accepted: 24 November 2012
Published: 30 November 2012
Genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers generate large quantities of tests results. Global and local graphical viewing of the test results is an effective approach to digest and interpret GWAS results.
SNPEVG is a set of graphical tools for instant global and local viewing and graphing of GWAS results for all chromosomes and for each trait. The current version includes three programs, SNPEVG1, SNPEVG2 and SNPEVG3. SNPEVG1 is a graphical tool for SNP effect viewing of P-values allowing multiple traits. The total number of graphs that can be generated by one ‘Run’ is n(c + 2), where n is number of ‘traits’ with 0 < n ≤ 100, and c is the number of chromosomes. SNP effect viewing and graphing is accomplished through a user friendly graphical user interface (GUI) that provides a wide-range of options for the user to choose. The GUI can produce the Manhattan plot, the Q-Q plot of all SNP effects, and graphs for SNP effects by chromosome by clicking one command. Any or all the graphs can be saved with publication quality by clicking one command. SNPEVG2 is for the viewing and graphing of multiple traits on the same graph with options to graph any or all of the traits, customizable colors and user specified Y1 or Y2 axis for each traits. The SNPEVG3 program uses the output file of single-locus test results from the epiSNP computer package as the input file. Each chromosome figure can display three genetic effects (genotypic, additive and dominance effects), and the number of observations.
The SNPEVG package is a versatile, flexible and efficient graphical tool for rapid digestion of large quantities of GWAS results with mouse clicks.
GWAS analysis generally yields large quantities of test results. Global and local graphical viewing of the test results is an effective approach and often is a necessary step for interpreting GWAS results. A widely used graphical viewing of GWAS results is the Manhattan plot, which provides a global graphic view of GWAS results of all chromosomes for a trait on one graph to quickly identify genome locations with the most significant SNP effects [1, 2]. Following this global view, detailed graphical examination of each chromosome is helpful for further understanding the GWAS results, and more graphical work often is needed for effective presentation of the GWAS results. The purpose of the SNPEVG package is to provide a graphical tool for rapid digestion of GWAS results and to accomplish large quantities of graphical tasks of GWAS analysis in a seamless fashion.
The SNPEVG computer package is implemented in the C++ programming language. The object orientation feature of the C++ language enables the efficient software development cycle by easy reuse of modules for different applications with similar features. The SNPEVG computer package used the Qt library under the terms of the GNU Lesser General Public License (LGPL) version 2.1 as shown .
Results and discussion
SNPEVG Version 3.2 includes three graphical programs: SNPEVG1, SNPEVG2 and SNPEVG3. SNPEVG1 is for graphing effects of one trait per graph for up to 100 traits, SNPEVG2 is for graphing multiple traits on the same graph, and SNPEVG3 processes directly uses an output file of EPISNP or EPISNPmpi  as the input file. Both SNPEVG1 and SNPEVG2 using the same format of the input file, which contain name, chromosome number and chromosome position of each SNP marker, and P-values of statistical tests from any method. Each program has a scalable GUI allowing efficient and flexible use of computer screen and allows the production of graphical images with user defined vertical/horizontal ratios. Each program can be launched multiple times by mouse click of the executable program so that the user can compare graphical effects of different graph options simultaneously. SNPEVG 3.2 is available from Additional files 1 and 2 or from the website at http://animalgene.umn.edu. Full features of the SNPEVG package are described in the SNPEVG user manual  Additional file 3.
The SNPEVG1 program
The SNPEVG2 program
The SNPEVGconvert program
The SNPEVGconvert program is designed to convert an output file from any GWAS analysis software to the format of SNPEVG1 and SNPEVG2. With this format conversion program, virtually any GWAS software could SNPEVG1 and SNPEVG2. To use this program, the user only needs to specify the number of columns in the original files and identify the column numbers to be printed in the input file for SNPEVG1 and SNPEVG2.
The SNPEVG3 program
SNPEVG3 is developed for graphical analysis of GWAS using the output file of single-locus test results of EPISNP or EPISNPmpi  as the input file for drawing figures. SNPEVG3 has similar GUI features as SNPEVG1, but it does not have the limit of 100 traits. This program draws graphs for P-values of additive, dominance and genotypic effects on the Y1 axis and draws sample size on the Y2 axis. The P-values can be displayed with lines connecting adjacent data points (Figure 3D) or use symbols without connecting lines (Figure 3E). The user has an option to draw a figure by a sorted effect such as additive or dominance effect.
Evaluation of sample size limitations
Processing time and limit of SNP markers for SNPEVG1 and SNPEVG3 of 32-bit (Windows 7) and 64-bit versions (Mac OS X) for one trait
Number of SNPs
Processing time and limit of SNP markers for SNPEVG1 and SNPEVG2 of 32-bit (Windows 7) and 64-bit versions (Mac OS X) for 100 traits
Number of SNPs
The SNPEVG package is a versatile and efficient graphical tool for rapid digestion of large quantities of test results from GWAS and can be customized for graphical viewing and drawing of non-GWAS information such as allele frequency differences.
Availability and requirements
Project name: SNPEVG
Project homepage: http://animalgene.umn.edu/
Operating system(s): Microsoft Windows 7, Mac OS X 10.6 or newer
Other requirements: none.
Any restrictions to use by non-academics: none.
Genome-wide association study
Single nucleotide polymorphism.
This research is supported by USDA National Institute of Food and Agriculture Grant no. 2011-67015-30333 and by project MN-16-043 of the Agricultural Experiment Station at the University of Minnesota.
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