haplotypeAnalysisPipeline

This pipeline prepares the population genotypes ped/map files, runs them on SHAPEIT, optionally uses the results as input for IMPUTE2 using the 1000G phase III reference panel, and finally converts them to Chromopainter_v2 formats in order to perform with fineSTRUCTURE fs 2.0.7 two clusterings of donors and recipients respectively, and with Chromopainter_v2 a painting of the resulting recipient clusters out of the donor clusters.