Phased - Unphased genotypes

Question

[mzezza]

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.

Answer 1

[Brian Bushnell]

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.