Phased - Unphased genotypes
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4.5 years ago
mzezza ▴ 10

Hi,

I would ask if someone could clarify me the concept of phased/unphased genotypes. In the first case we know the haplotype and in the second case we don't know the haplotype ?

Thanks.

SNP gene impute phased genotypes haplotypes • 2.7k views
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Entering edit mode
4.5 years ago

You know the haplotypes in each case. The difference is that for phased heterozygous variants, you know which variants are on the same chromosomal copy. For example, take heterozygous variant 1 (A/C) and variant 2 (T/G). One chromosome copy will have an A at location 1, and the other will have a C. But what allele will be present at location 2 for the chromosome copy with an A at location 1? With unphased variants, you don't know - could be T or G. With phased variants, you know which one it is. Phasing is not necessarily complete; often you can only phase small regions.

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