I created a text file as defined in Appendix A of GenABEL manual, but I keep getting the message
Reading genotypes from file './genotype_illumina.txt' ...
Error in convert.snp.illumina(inf = "./genotype_illumina.txt", out = "./gen0i.raw", :
illegal genotype (three alleles) for SNP 'NC0199888' (line 2)!
Bellow the first three rows of my file
name chr pos strand RADA017 RAFU002 RAFA001
NC0199888 1 100 u AA AA AA
NC0200507 1 100 u AA AA AA
NM0325430 1 800 u BB AA BB
I checked many times if exists some genotyped with three alleles and it not exists.
Thanks in advance!