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Open Access Highly Accessed Software

SNPEVG: a graphical tool for GWAS graphing with mouse clicks

Shengwen Wang, Daniel Dvorkin and Yang Da*

Author affiliations

Department of Animal Science, University of Minnesota, St. Paul, USA

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Citation and License

BMC Bioinformatics 2012, 13:319  doi:10.1186/1471-2105-13-319

Published: 30 November 2012

Abstract

Background

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.

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.

Conclusions

The SNPEVG package is a versatile, flexible and efficient graphical tool for rapid digestion of large quantities of GWAS results with mouse clicks.