Question: PLINK error message
gravatar for alhamidi.reem
20 days ago by
alhamidi.reem0 wrote:

Hi everyone,

I am new to PLINK and I have a few problems that I cam across as some users have.

I currently downloaded a ped and map files from the ensemble website which were converted to ped from vcf format. I unzipped the .gz file and i can access the ped and map perfectly fine.

However, when I try to create a bed file for that particular file that was downloaded, I get this message:

ERROR: Locus rs4286970 has >2 alleles:

       individual CEU_4 NA12154 has genotype [ 2 3 ]
       but we've already seen [ 3 ] and [ 1 ]

Bear in mind, when I downloaded the map file, there were only two coloumns available (the SNP ID and bp location) so i added 2 new columns manually (chromosome number and the genetic distance). The genetic distance was coded to 0 for all rows.

how can I create a bed file?

ADD COMMENTlink modified 20 days ago by finswimmer10k • written 20 days ago by alhamidi.reem0
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: 1689 users visited in the last hour