Hello fellow Biostars,
I am currently aiming to impute genotypes from different SNP-Chip resolutions (6k, 50k, 777k...) and have tried Beagle 4.0 and FImpute because I want to include pedigree information.
The process seems successful so far, however, FImpute notifies me that changes to the original genotypes have been made (due to mendelian errors I presume). As far as I know there is no way to prevent the programme from doing so.
Beagle on the other hand never gave a warning or other that genotypes have been altered - I tried checking and have the feeling that it doesn't happen.
Do you know if Beagle (4.0) also changes genotypes during imputation if it encounters pedigree/ mendelian errors?