A flexible tool to plot a genomic map for single nucleotide polymorphisms.

BACKGROUND: Most genetic association studies use single-nucleotide polymorphisms (SNPs) as the research targets. However, resources to visualize the genomic map of candidate SNPs in a programming manner are limited. We have previously created an R package, mapsnp v0.1, to plot the genomic map for a panel of SNPs within a genomic region of interest. It failed to work under the latest version of Gviz package.

RESULTS: We updated the mapsnp package to keep up with the latest package environment and improved its functionality by adding more parameters to fine tune plotting outputs.

CONCLUSIONS: The mapsnp package is a flexible software to visualize genomic map for SNPs, involving the relative chromosome location and the transcripts in the region.