This contains the development of the genotypeR R package. genotypeR implements a common genotyping workflow with a standardized software interface. genotypeR designs genotyping markers from vcf files, outputs markers for multiplexing suitability on various platforms (Sequenom and Illumina GoldenGate), and provides various QA/QC and analysis functions. This package can be installed from the github repository using devtools. This package will also be avaliable on CRAN, and can be installed in the usual way.
If it is desirable to only use the PERL pipeline without the rest of the R package that is possible as well.