Probability of genotypes with AlphaImpute2 #24
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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. |
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Replies: 2 comments
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Hi @Leo4Luffy, 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. You have two options:
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@Leo4Luffy I have opened an issue for this at #25 |
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Hi @Leo4Luffy,
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. You have two options:
Play with call thresholds
Look into calling code and output the underlying probabilities