Quality control after genotype imputation

Question

[jzannatun]

Can anyone kindly explain me the possible ways of quality control of imputed data? Any reference papers or site describing post imputation quality control would be highly appreciated. I am quite new in this field. I have used BEAGLE for imputation. Thank you in advance.

[jean.elbers]

Different programs such as BEAGLE and IMPUTE2 have different guidelines for post imputation quality control, which I am not an expert on. Those who might be able to help you would benefit from knowing what program you used for imputation to guide responses to you.

[jzannatun]

Dear jean.elbers I have used BEAGLE for imputation

[jean.elbers]

This article may be of help - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137601

[jzannatun]

Thank you. I am reading the article.

Answer 1

[jean.elbers]

So, someone else chimed in on BEAGLE post imputation quality control, see A: Beagle imputation results quality control

[jzannatun]

Thanks a lot! I hope I can finish my work soon.