RoH for nonmodel species aligned to closely related reference (exomes)

[eggomez]

Hi there,

Thank you for a great program! I don't exactly have an issue, but I am hoping for a sanity check on RoH so I can feel confident in my analysis since I am using an atypical dataset but I think the tools is appropriate.

I have nonhuman primate exome data (since exome capture works well for primates), but it is aligned to a congener reference assembly. I think this is fine since I have ~30 individuals from the same populations so I can estimate allele frequencies from my data so I am assuming that fixed differences between species will not lead to overestimates of homozygosity.

Also, I am getting RoHs that are longer than what is continuously represented in the exome, but my understanding is that this is what is supposed to happen - that the exome data are essentially being used as marker data and that the HMM takes into account their discontinuousness and sparsity...it's just a little weird to wrap my head around.

Thank you for any thoughts on whether bcftools roh would be appropriate. This is an endangered species, so this is meant as a conservation genetics analysis (looking at inbreeding, possible bottleneck, and potentially inbreeding depression as enrichment of deleterious variants in ROH). Thank you!!