how to deal with 0 in allele from ped/map files

Question

[Victor]

Hello,

I have a ped/map files generated from illumina final report by perl script.

Then I found out that I have many "-" in the allele1 or allele2. I check the perl script and the script will make "-" into "0".

Anyway, I am doing the position selection and I dont need the 0 in my plink file (raw data). So I try to remove the 0 from plink file by geno 0.1 or snps-only just-acgt. However, I still can find 0 in the allele.

I know this may or maybe someone had poster at somewhere. Please let me know if you have any suggestions for this.

Many thanks