Imputation of X chromosome non-PAR for male subjects

Question

[Apprentice]

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?

Answer 1

[adriano.demarino]

Hi,

If you want to convert your haploid genotype in diploid just do it using bcftools +fixploidy:

bcftools +fixploidy {vcf_file} -- -s {ploidy_file} 

where {ploidy_file} is something like:

sample_name1 M
sample_name2 F

where M --> MALE , F --> Female.

Cheers,

Adriano from SelfDecode

[Apprentice]

I'm sorry for my late reply. Thank you for your advice.

My data is imputed genotype. So, the imputed data is coded as [0,1], and continuous values. This method that you suggested is available for the imputed data?