How to get imputation accuracy/quality after using IMPUTE2?

Question

[Wan Shi Tong]

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!

Answer 1

[Wan Shi Tong]

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

[Charles Warden]

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).