The bash script reformats shapeit .haps file to show samples by rows instead of variants by rows
bash shapeit.reformat.sh in_ped in_haps out_haps out_map
in_ped --> .ped file that shapeit takes as input
in_haps --> .haps file that shapeit outputs
out_haps --> name of the output .haps file, which contains the same info as in_haps but with the samples distributed by rows
out_map --> name of the output .map file