Ensembl Variation REST API Phased Haplotype?

Question

[johntimcham]

I am using the Ensembl REST API to access variation data for a selection of SNPs. The output for each allele is in the form "G|A" for each rs# that I provide. Suppose for two SNPs the output is "G|C" and "A|T". Does this mean that one chromosome has the G and A variants while the other chromosome has the C and T variants?

This seems like it should be the case given that a "G|C" will also pop up as "C|G" for a different sample for the same rs#.

Thanks,

Answer 1

[Emily]

If you're getting individual genotypes, then yes, the pipe means that it's phased.

[finswimmer]

I often read the term "phased genotype", but couldn't figure out what this means exactly. Can someone please enlight me.

fin swimmer

[Emily]

If genotypes are phased it means we know which of the homologous chromosomes they're on. Let's say I had two variants on chromosome 1 and the genotype for an individual for the first was A|T, and the genotype for the second was G|T. If they're phased (which is what the vertical pipe | means) then I know that A and G are both on the same chromosome, and T and T are both on the same chromosome. This allows me to do things like calculate LD or determine the actual sequence of the genes/proteins in that individual.

If, however, those two genotypes were listed as A/T and G/T, that means they are not phased, I don't know which chromosome is which and I can't calculate LD etc.

[finswimmer]

Thanks a lot for your explanation. Now I got it :)