I have plink (affymetrix) input data in .ped/.map files which is unfiltered and needs the params found below, I have also added filtering for HWE and missingness, however I want to get the same output format as I put in, so I can use the file in my R script.
How can I get --compound-genotypes in my output?
--no-sex PED file does not contain column 5 (sex)
--no-parents PED file does not contain columns 3,4 (parents)
--no-fid PED file does not contain column 1 (family ID)
--no-pheno PED file does not contain column 6 (phenotype)