SNPEVG: a graphical tool for SNP effect viewing and graphing

SNPEVG is a set of graphical tools for SNP effect viewing and graphing. The current version includes two programs, SNPEVG1 and SNPEVG2. SNPEVG1 is a graphical tool for SNP effect viewing and graphing for rapid digestion of large quantities of genome-wide significance test results using P-values from any methods of significance testing. Assuming 30 traits and 30 chromosomes per trait, one command of ‘Run’ produces 960 graphs that will greatly facilitate the digestion of genetic analysis results. 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. Any of the graphs could be readily placed in a publication. 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 as png files by clicking one command. The program allows users to select traits for graphing and viewing. The SNPEVG2 program currently uses the output file of single-locus test results from the epiSNP computer package as the input file for drawing figures. Each chromosome figure can display three genetic effects (genotypic, additive and dominance effects) and the number of observations.