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24 months ago
@alhamidi.reem52131

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?

PLINK software error genome snp gene • 239 views
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What is the command that you are using to convert ped to bed ?