You can use calc_imp_acc.py to calculates imputation accuracies for SNP markers as presented in Calus et al (2014; https://doi.org/10.1017/S1751731114001803). The imput files needs to be in the BLUPF90 format (http://nce.ads.uga.edu/wiki/doku.php?id=readme.pregsf90).
In addition, you can use the imp_acc_results.R script to plot the imputation results from the above Python program.
Any question fell free to ask Andre C. Araujo: andre.araujo@acufastswine.com/andrefuturo7@hotmail.com/araujoandrecampelo@gmail.com