Question: Error: Line 2 of .ped file has more tokens than expected.
1
gravatar for sonia.olaechea
6 months ago by
sonia.olaechea60 wrote:

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

plink snps • 557 views
ADD COMMENTlink modified 6 months ago by zx87547.1k • written 6 months ago by sonia.olaechea60

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.

ADD REPLYlink written 6 months ago by zx87547.1k
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