Question: how to deal with 0 in allele from ped/map files
gravatar for Victor
20 months ago by
Victor10 wrote:


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

map ped plink • 432 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by Victor10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1945 users visited in the last hour