Dear All, I am trying to phase my vcf file that contain one population of five individuals and generate .hap file with shapeit. The problem that I am encountering is that shapeit will not run and instead require a reference panel because the number of individuals is less than 100. Is it possible to run shapeit with only these individuals and how would I produce a reference panel, please? By the way, I am working on chickens genome.
Your help would be appreciated.