Hello,

I am looking to create a reference set of samples based off of their relatedness. I need the reference set to be used to impute using Beagle. I previously have used some plink1.9 to create the reference set. But I was curious what other people more experienced in the field have used. Is there a software package/packages that people have good results with to create a reference set?

VCFtools looked promising, you can get the relatedness of the samples but can't easily filter them based on some threshold. Any suggestions could help!

Thanks, Sean