<p><em>Answer from @user438383, converted from comment:</em></p>
<p>I would recommend checking out <a href="https://odelaneau.github.io/shapeit4/" rel="nofollow noreferrer">shapeit4</a> as it is able to integrate statistical phasing and read-based phasing like you are after. The manual page for WhatsHap might also be useful for you:</p>
<p><a href="https://whatshap.readthedocs.io/en/latest/index.html" rel="nofollow noreferrer">https://whatshap.readthedocs.io/en/latest/index.html</a></p>

CC BY-SA 4.0
2021-07-14T11:14:23.450Z
2021-07-14T11:14:23.450Z
gringer
<p>I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array.  I would like to merge the data together in the correct phase.  Since the exomes are already phased with read informed phasing, I don't want to rephase them because some of the phasing changes after doing this.  Is there a way to statistically phase genetic data that has already been partially phased?</p>
<p>My data is in VCF format.</p>
<p>Thanks</p>

<genomics><genotyping><exome><phasing>
Phasing partially phased genomic data
# Phasing partially phased genomic data

(Asked by: username_0 on 2020-03-29)

I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array. I would like to merge the data together in the correct phase. Since the exomes are already phased with read informed phasing, I don't want to rephase them because some of the phasing changes after doing this. Is there a way to statistically phase genetic data that has already been partially phased?

My data is in VCF format.

Thanks

**Tags:** genomics, genotyping, exome, phasing

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## 1 answers

### Answer by username_1 on 2021-07-14. Score: 1

*Answer from @user438383, converted from comment:*

I would recommend checking out [shapeit4](https://odelaneau.github.io/shapeit4/) as it is able to integrate statistical phasing and read-based phasing like you are after. The manual page for WhatsHap might also be useful for you:

<https://whatshap.readthedocs.io/en/latest/index.html>


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