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!
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written
by
miaowzai
1 answer
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.
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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