what is 0 in the plink .bim file under allele1/2 column?
1
1
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3.9 years ago
miaowzai ▴ 280

Hello,

I have a bfile data that contains zero "0" in the allele column in .bim file. Both allele columns contain SNPs recorded as "0". I didn't find corresponding descriptions on plink website. Does it mean unknown allele? Why is there such thing?

example:

1 rs123 0 242345 0 A

1 rs234 0 24532 0 0

Thanks!

plink allele microarray array chip • 3.3k views
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3.9 years ago

In a .ped + .map fileset, it's possible for a variant to have only one distinct allele (everyone's A A or 0 0), or even zero (everyone's 0 0). If a .bim file is generated from this type of data, it'll have 0 in place of each unknown allele code.

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May I ask why this happens? Thanks!

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Consider the simplest case, where you have just one sample. Whenever the sample has a homozygous call, you'll only see one allele code. Whenever it has a missing call, you won't see any allele codes.

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