Question: PLINK error message
gravatar for alhamidi.reem
4 months 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 3 months ago by Biostar ♦♦ 20 • written 4 months ago by alhamidi.reem0

What is the command that you are using to convert ped to bed ?

ADD REPLYlink written 3 months ago by Inquisitive8995100
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