I know I might be missing something obvious, but how do I get the accuracy/quality of my imputation after using IMPUTE2 (or any imputation tool)? How is the quality of an imputation measured?
Thank you!
I actually figured it out. Incase anyone ever has the same question. IMPUTE2 outputs a file called info where it has imputation quality information. Depending on the command line arguments you choose you can get more specific statistics. https://mathgen.stats.ox.ac.uk/impute/output_file_options.html#info_metric_details
If at all possible, I think you should also try analysis strategies that don't require imputation, but I appreciate your feedback (I was not familiar with that link).
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