PSMC: create pseudo-diploid male X chromosomes from different species

Question

[yorgos.athanasiadis]

Hi,

I have male X chromosome data in fq format from different ape species and I was wondering if there is an existing method to merge them in order to create pseudo-diploid X chromosomes for PSMC analysis?

Note that some loci in the consensus sequence appear as polymorphic, so my guess is that I first have to mask those out?

Thanks!

Yorgos