text: user8875: 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?
  
  user3694: HaploSep uses allele frequency data - I presume you have genotype data.
  In that case, I would suggest looking at either Beagle5.2, shapeit4 and Eagle2. I believe they more or less give the same accuracy (Eagle2 is slightly less accurate than the other two) and Beagle 5.2 is faster than the rest. Depending on what you plan on doing with the haplotypes, I don't think that the choice of phasing algorithm will affect downstream results a great deal.
  
original_text: 8875: <p>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.</p>
  <p>I have a VCF/PLINK format file of ~8,000 individuals with ~150,000 SNPs each (from across a population with several sub-populations).</p>
  <p>I want to use the resulting data to place new samples into one or more populations (e.g. ancestry analysis).</p>
  <p>Before I go trying to make one of these tools work / look at accuracy, etc., am I doing it right in the first place?</p>
   3694: <p>HaploSep uses allele frequency data - I presume you have genotype data.</p>
  <p>In that case, I would suggest looking at either <a href="https://faculty.washington.edu/browning/beagle/beagle.html" rel="nofollow noreferrer">Beagle5.2</a>, <a href="https://odelaneau.github.io/shapeit4/" rel="nofollow noreferrer">shapeit4</a> and <a href="https://alkesgroup.broadinstitute.org/Eagle/" rel="nofollow noreferrer">Eagle2</a>. I believe they more or less give the same accuracy (Eagle2 is slightly less accurate than the other two) and Beagle 5.2 is faster than the rest. Depending on what you plan on doing with the haplotypes, I don't think that the choice of phasing algorithm will affect downstream results a great deal.</p>
  