search

zhengxwen / HIBAG

R package – HLA Genotype Imputation with Attribute Bagging (development version only)
https://hibag.s3.amazonaws.com/index.html
29 stars 7 forks source link

Imputed genotypes to train HIBAG Models? #12

Closed adiamb closed 3 years ago

adiamb commented 4 years ago

Hello, Its not really an issue, but wonder if we can use imputed genotypes to train a HIBAG model? If so what are pros and cons of this approach in relation to using the genotyped snps? thank you for this fantastic package Aditya

zhengxwen commented 4 years ago

I would suggest using directly genotyped SNP data to avoid low-quality imputed genotypes (especially rare variants).