Hi,
When I look into the WGS files there are no genotypes for the annotated variants, is there a way of getting these? In the all variants VCF files there are the genotypes.
Additionally if possible could you please clarify to me what the score for each rsID is for the imputed genotypes? It was not really clear to me what this score represents? Ultimately I am trying to get the genotype for the ROSMAP study participants in the 0, 1 or 2 format. Would this score be suitable to modify using plink into this?
Thank you very much for your help.
Ashley
Created by Ashley Heinson Ashley_Heinson Ashley-
I'm confused about your issue with the WGS data. Can you give some specific examples?
Imputed genotypes are reported as dosages. Because they are computed based on the imputed genotype probabilities, they will be integer valued only when the exact genotype is known (i.e. at directly assayed loci). Otherwise they can take continuous values between 0 and 2. These files can be read into Plink. See the [documentation](http://zzz.bwh.harvard.edu/plink/dosage.shtml) for details.
Solly
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