I am working on the population genomics of a mosquito species and have around 300 whole genomes from one species sampled from several populations. Coverage is 30X per genome and genome size is ~180Mbp.

My questions are:

1) Is it appropriate to include all populations when attempting to phase genomes? (using for example SHAPEIT5)?

2) How many samples are needed to accurately phase genomes (overall and per population)?

3) Any suggestions on the best program/s to use for phasing?

Thank you!!