Hello Biostar,

I was wondering what the fastest and best way to get from VCF4.1 --> population substructure is and how much consensus there is on how much the appropriate solution depends on one's cohort.

In other words, has the field reached agreement on how the size, ancestry, and other parameters of a given cohort should shape tool choice for conversion, or on how many low frequency variants should be included?

Thank you very much in advance.