Modified germline utilities scripts to convert Beagle file format to PED format
This code was modified from the germline pipeline from utilities published by Gusev et al in Whole population, genome-wide mapping of hidden relatedness which was released under the GPL license. It essentially modifies the phasing pipeline to convert beagle files straight to ped files without passing files through the germline program.
Original Phasing Pipeline can be found here
Included in this repository are the original README, makefile, convertion C++ code, and modifies shell scripts.