interval for sex chromosomes

[Homap]

Hello,

I was wondering how I could use the interval program of LDhat to generate sex-averaged rho for sex chromosomes where females are diploid and males are haploid?

Having 5 males and 5 females for such sequence, I essentially have 5 X chromosomes in males and 10 X chromosomes in females. When creating the sites file, how should I indicate that?

Would it be wrong if I make the haploid data pseudo-diploid, that is imagining A is AA and code it accordingly as a homozygous genotype?

Thank you in advance, Homa

[auton1]

When faced with this problem a long time ago, I believe we just used the female individuals to estimate recombination rates. Treating the males as diploid will likely lead to biased estimates. An alternative option may be to combine the haploid males to create artificial diploid individuals, which I think might be a better option, although I have not tested this.

On Fri, 10 Jun 2022 at 06:50, Homa Papoli Yazdi @.***> wrote:

Hello,

I was wondering how I could use the interval program of LDhat to generate sex-averaged rho for sex chromosomes where females are diploid and males are haploid?

Having 5 males and 5 females for such sequence, I essentially have 5 X chromosomes in males and 10 X chromosomes in females. When creating the sites file, how should I indicate that?

Would it be wrong if I make the haploid data pseudo-diploid, that is imagining A is AA and code it accordingly as a homozygous genotype?

Thank you in advance, Homa

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[Homap]

Thanks a lot for your reply. That makes a lot of sense. I'd like to obtain the sex-averaged recombination rate but I just thought that since X does not recombine in males anyway, total recombination rate for sex chromosome is equal to female recombination rate. I could, as you said, just use the females and obtain the sex averaged recombination rate by multiplying the X recombination rate by 2/3. Thanks a lot again.