This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Imputation for genotyping data

The imputation method used to impute genotype is usually used for GWAS data. Can this be used for genotyping data with small samples of 20 in number

gentyping imputation

1 answer

As inferred in this paper

In principle, a phasing algorithm should be able to “learn” about desirable phasing configurations for a given study individual by pooling information across the reference panel and all other individuals in the study, and the phasing accuracy should increase with the sample size; in standard practice, most imputation methods gain phasing information about each study individual only from the reference panel, and phasing accuracy does not depend on the size of the study sample.

I would say, it is generally possible. It could be that the accuracy is lower than using a higher sample size. Nevertheless, I suggest to run for example the Imput2 pipeline and check the quality afterwards (e.g. info and certainty score).

Log in to answer this question.