I have a vcf file that I am aiming to impute using IMPUTE2. I will mask some selected SNPs. My question is since I have the ground truth and the imputed result, how do I evaluate the quality of the imputation?
read the impute2 manuscript, or other articles on masked results. the impute2 algorithm will generate these for you on a by chromosome or by block or by input file basis (cant remember which)
Thank you so much. This makes sense.
yeah no problem. that is how the quality metrics are being calculated - they take a snp that they actually have genotyped, and impute it.
then, they check to see how accurate they were. this serves as a useful estimate for nearby variants nearby that have the same characteristics (that actually are only imputed).
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