If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.

  • 2
    $\begingroup$ What method do you want to use - this likely makes a difference. $\endgroup$
    – user438383
    Oct 10, 2023 at 8:36
  • $\begingroup$ @user438383 Beagle/Eagle $\endgroup$
    – BigMistake
    Oct 10, 2023 at 17:56
  • $\begingroup$ @user438383 but I'd also be interested in other methods if someone happens to know those too $\endgroup$
    – BigMistake
    Oct 10, 2023 at 17:56

1 Answer 1


Yes. Phasing data leads to a better imputation accuracy. More specifically:

  • Improves allele matching: Correct phased data ensures that alleles are matched correctly between the reference panel and the target dataset.
  • Using phased data, the computational time of imputation is significantly reduced.
  • Having haplotypes (phased data) helps imputing variants that were not genotyped (missing variants/genotypes).

This paper based on the UK10K data has some actual numbers describing imputation accuracy of phased vs unphased data.


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