By developing the this framework we attempt to reduce on the one hand the number of false positive calls and on the other hand reduce the number of filtered positive calls. \cite{Torkamaneh_16} did conduct a comparative analysis of different existing GBS pipelines. However, the above mentioned issue was not addressed but provided excellent groundwork for further analytical as well as developmental work. We would, therefore, like to build on this work and intend to test the variant calling pipelines with both real data and simulated data. Moreover, the simulated data will be constructed by applying a permutation process so as to examine the affects of different forms of bias and errors on the alignment and variant calling processes. To date, this kind of analysis has not been done and is the critical element for establishing an interpretive context. The work done within this proposal will not only provide a foundation in terms of developing a software framework, it will also develop the analytical skill sets necessary to generalise the methodology to other variant calling pipelines and workflows. Further, as we explore previously unanalysed data in the realm of polyploids the aligners and variant callers used may behave in unexpected ways. Charting the behaviour of these tools using simulated data will position PFR well in the emerging field of polyploid analytics.