I'm new both to the forum and to using Plink so I will start with a question related to this software:
I'm trying to split a .ped file by chromosomes and running the following command in bash:
for chr in $(seq 1 22);do plink --file myfile --chr $chr --no-pheno --no-sex --no-parents --make-bed --out myfile.chr$chr ; done
However, I get the following error:
Error: Line 2 of .ped file has more tokens than expected.
I've observed that some of my positions in the genotype column have more than 2 alleles, e.g.: - -
CC CC TTTCTCCCCGGCCTGCTTG
Could this mistake be related to it? If so, how can I solve it?
Thank you very much in advanced!