Question: Allele coding BIM and Genotypes in SNPmatrix (0,1,2,3). Coding doubt.
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2.5 years ago by
j.j.stocks0 wrote:

Hi, I have the following situation for a SNP:

In the BIM file Contig position A1 A2 3551 58921 C T

Reference is T

In the SNPmatrix it gets coded as 3 when T/T and 1 when C/C, 2 T/C.

Given the reference is T and for individuals that are T/T shouldn't it be coded 1?

Many thanks

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