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refine population phased haplotypes by pedigree

I have ~5000 15X WGS samples phased without reference using Eaglev2. Now I got pedigree information about a small number of the samples (trios and duos). I would like to improve the phasing of the children. Since the number of samples with pedigree information is small, phasing the samples again using SHAPEIT is not worth the time and resources. Is there a software or method that can improve existing phased haplotypes with newly acquired pedigree information?

phasing genotype pedigree population
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updated by bmstudent • bmstudent • written by samuelandjw • samuelandjw

1 answer

You might want to look at BEAGLE as it can handle pedigree information with pairs and trios

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written by bmstudent • bmstudent

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