Question: Allele coding BIM and Genotypes in SNPmatrix (0,1,2,3). Coding doubt.
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j.j.stocks • 0 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