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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

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Answer from @user438383, converted from comment:

I would recommend checking out 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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