Error: Line 2 of .ped file has more tokens than expected.

Question

[biosol]

Hi all,

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!

Sonia

[zx8754]

There is a mismatch with number of SNPs in map file and number of SNP columns in ped file. Ensure you have standard 6 columns then SNP columns in your ped file. Or if, for example, parents columns missing then use --no-parents flag to indicate that.