0
$\begingroup$

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

$\endgroup$
3
  • 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

5
$\begingroup$

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.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.