Output posterior probabilities for alleles and genotypes

[gregorgorjanc]

Discussed in #24

^{Originally posted by Leo4Luffy July 19, 2023}
Good morning, I hope you are very well. I just wanted to ask a little question. I have performed the imputation of genomic data using AlphaImpute2. I have used the three proposals of this program: imputation based on the pedigree, imputation based on the population and imputation using both sources of information. From this, I have obtained the genotypes in phase and the imputed genotypes. I wanted to ask you, and excuse me, if AlphaImpute2 also allows you to obtain the probability of genotypes as AlphaImpute does? I would appreciate any information you can give me. A happy day.

[gregorgorjanc]

The model and algorithms behind AlphaImpute2 are probabilistic https://www.biorxiv.org/content/10.1101/2020.09.16.299677v1, but (to my understanding) output are called alleles and genotypes. While a user can 1) Play with call thresholds it could be useful to 2) output the probabilities that underlie the calls, hence this issue.