Dear all I am using –score function in plink to generate polygenic risk score. Against the –score function I have supplied .raw file which contains: (1) RS id, (2) AFFECT allele & (3) corresponding log (OR). The output file (.profile) contains: (1)FID, (2)IID, (3) PHENO, (4)CNT (5)CNT2 and (6) SCORE. I am interested in to also get the information on “total number of RISK alleles” against each individual. Is there a way to get this information in Plink? I cannot take the CNT2 count, as this is the count of the number of AFFECT alleles (from the supplied .raw file and some alleles will be protective since the OR are <1). Is there a way to get this information by adding any option after the –score function in plink? Thanks