What is the best option?

[glaudelrio]

Hi, I am trying to evaluate whether chromosomal inversions in a genome are under selection or no. I thought about calculating piN and piS within and outside inversions.

My target system is a hybrid zone with two bird species, and the inversion states differ across species with heterokaryotypes in the center of the hybrid zone. What is the best approach here? Work with alignments or provide a VCF with individuals in the two species and hybrids?

Thank you so much for nay help!

[singing-scientist]

Greeting, Glaucia!

Personally, anytime I can keep things simple and AVOID use of VCF files, that's what I choose. One reason is for my own sanity: there may be things I want to examine in the sequences themselves, which becomes difficult if one has to perform the extra step of examining the VCF. Because it seems you will be sequencing individuals (not deep-sequencing pools of individuals), I would therefore opt for a simple FASTA multiple sequence alignment (MSA). Another benefit is that this will preserve LINKAGE information of any variation, which VCF does not (at least, not beyond one codon). Finally, a MSA would also make your data amenable to examination by many more tools than VCF will.

Let me know if that helps!