Sex determination using bcftools

Question

[Mohadese]

How to determine the sex of individuals using only one single chromosome X vcf file using bcftools?

Answer 1

[Pierre Lindenbaum]

X and only X ? not tested:

I would look at the mean DP in the PAR regions and compare it to the sexual region. DP(PAR)=2*DP(SEX) with men.

[Mohadese]

Then how do people determine sex using bcftools? Do they merge all the chromosomes together? I am new to the field so if it's possible please explain more.

[Pierre Lindenbaum]

your question is not clear at all. I read it like you have a vcf with only chrX. Otherwise there is

bcftools +guess-ploidy 

Determines sample sex by checking genotype likelihoods (GL,PL) or genotypes (GT) in the non-PAR region of chrX.

[Mohadese]

As input of this bcftools command, I have put a vcf containing all autosomal chromosomes + chromosome X, right? I thought that I should use non-PAR region of chrX as the input of this command.