<p><a href="https://odelaneau.github.io/shapeit4/" rel="nofollow noreferrer">shapeit4</a> is currently (probably) the most accurate and quickest phasing algorithm which can account for sequencing reads in the model. They suggest you extract the phase information from the reads using <a href="https://whatshap.readthedocs.io/en/latest/" rel="nofollow noreferrer">WhatsHap</a> first however. The guide for WhatsHap can be found <a href="https://whatshap.readthedocs.io/en/latest/guide.html" rel="nofollow noreferrer">here</a> and has some info on using data processed using GATK. </p>

CC BY-SA 4.0
2020-01-10T18:04:13.090Z
2020-01-10T18:04:13.090Z
user438383
<p>I'm wondering if there are any tools out there that perform statistical phasing of genetic data (e.g. Eagle) that take read-based phasing from GATK into account.  I've found <a href="https://academic.oup.com/bioinformatics/article/35/14/i242/5529122" rel="nofollow noreferrer">this paper</a> which sounds like what I am looking for, but that tool was developed specifically for Hi-C data, and I only have exomes.</p>

<p>Thanks</p>

<exome><genetics><phasing>
Read-informed statistical phasing
# Read-informed statistical phasing

(Asked by: username_0 on 2020-01-06)

I'm wondering if there are any tools out there that perform statistical phasing of genetic data (e.g. Eagle) that take read-based phasing from GATK into account. I've found [this paper](https://academic.oup.com/bioinformatics/article/35/14/i242/5529122) which sounds like what I am looking for, but that tool was developed specifically for Hi-C data, and I only have exomes.

Thanks

**Tags:** exome, genetics, phasing

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## 1 answers

### Answer by username_1 on 2020-01-10. Score: 1

[shapeit4](https://odelaneau.github.io/shapeit4/) is currently (probably) the most accurate and quickest phasing algorithm which can account for sequencing reads in the model. They suggest you extract the phase information from the reads using [WhatsHap](https://whatshap.readthedocs.io/en/latest/) first however. The guide for WhatsHap can be found [here](https://whatshap.readthedocs.io/en/latest/guide.html) and has some info on using data processed using GATK.


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