I have a ped and a map file with 90 populations, and I wish to perform a MAF filter on each of those populations separately, using PLINK. The final output could be individual outputs for each family or in the best scenario, a dataset with the variants remaining (or excluded) from each of the families.
Should I first split the map and ped files in 90 other map and ped files (one for each family) and then execute the PLINK command for each of the populations? Or is there a way for PLINK to do both of these steps at once?
Thanks in advance!