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?
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
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?
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