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AlphaGenes / AlphaImpute2

AlphaImpute2: pedigree- and population-based genotype imputation
MIT License
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Output posterior probabilities for alleles and genotypes #25

Open gregorgorjanc opened 1 year ago

gregorgorjanc commented 1 year ago

Discussed in https://github.com/AlphaGenes/AlphaImpute2/discussions/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 commented 1 year ago

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.