<p>Yes. <a href="https://www.mdpi.com/2075-1729/12/12/2030#B16-life-12-02030" rel="noreferrer">Phasing data leads to a better imputation accuracy</a>. More specifically:</p>
<ul>
<li>Improves allele matching: Correct phased data ensures that alleles are matched correctly between the reference panel and the target dataset.</li>
<li>Using phased data, the computational time of imputation is significantly reduced.</li>
<li>Having haplotypes (phased data) helps imputing variants that were not genotyped (missing variants/genotypes).</li>
</ul>
<p><a href="https://www.nature.com/articles/ncomms9111" rel="noreferrer">This paper</a> based on the UK10K data has some actual numbers describing imputation accuracy of phased vs unphased data.</p>

CC BY-SA 4.0
2023-10-11T09:23:58.907Z
2023-10-11T09:23:58.907Z
JRodrigoF
<p>If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.</p>

CC BY-SA 4.0
2023-10-10T08:36:55.407Z
What method do you want to use - this likely makes a difference.
user438383
CC BY-SA 4.0
2023-10-10T17:56:22.103Z
@user438383 Beagle/Eagle
BigMistake
CC BY-SA 4.0
2023-10-10T17:56:42.520Z
@user438383 but I'd also be interested in other methods if someone happens to know those too
BigMistake
<microarray><wgs><imputation><phasing>
Does phasing improve imputation quality?
# Does phasing improve imputation quality?

(Asked by: username_0 on 2023-10-10)

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

**Tags:** microarray, wgs, imputation, phasing
> **Comments:**
> **username_1**: What method do you want to use - this likely makes a difference.  
> **username_0**: @user438383 Beagle/Eagle  
> **username_0**: @user438383 but I'd also be interested in other methods if someone happens to know those too  

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## 1 answers

### Answer by username_2 on 2023-10-11. Score: 6 | Accepted answer

Yes. [Phasing data leads to a better imputation accuracy](https://www.mdpi.com/2075-1729/12/12/2030#B16-life-12-02030). 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](https://www.nature.com/articles/ncomms9111) based on the UK10K data has some actual numbers describing imputation accuracy of phased vs unphased data.


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