I think Eagle or haploSep will do the job of reconstructing haplotype data, but I'm not sure what the 'standard' or best practice tool to use is...
I have a VCF/PLINK format file of ~8,000 individuals with ~150,000 SNPs each (from across a population with several sub-populations).
I want to use the resulting data to place new samples into one or more populations (e.g. ancestry analysis).
Before I go trying to make one of these tools work / look at accuracy, etc., am I doing it right in the first place?