Imputation of X chromosome non-PAR for male subjects
Hi.
I did an imputation of X chromosome SNPs for male subjects by using Minimac3.
I got a vcf file of the imputed SNPs.
The males on the non-pseudoautosomal part of the X chromosome were coded as 0 or 1.
However, I hope that males on the non-pseudoautosomal part of the X chromosome were coded as 0 or 2 (all genotypes as diploid homozygotes).
Could you how to do it?
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