Comparing Beagle, Impute2, And Minimac Imputation Methods

Question

[Maxime Lamontagne]

Hi everyone,

Golden Helix posts on their blog a comparison of various imputation methods: "Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory Usage".

Do you think they did a good job?

Do you find their results useful?

Did they forget something important?

I just want your opinion because sometime I'm lost with all these methods/software.

Thanks
Maxime

Answer 1

[Kantale]

I think this is one of the most thorough and independent comparisons out there. All the authors of imputation software (IMPUTE2, BEAGLE and MACH) have performed some sort of comparison in their papers pinpointing marginal benefits for their respective tools. The bottom line of golden helix' comparison is:

• Neither tool distinguishes itself as superior.
• In case of IMPUTE2 you have the benefit of multiple reference panels + you don't have to care about population composition in the reference panel.

EDIT:

Another very good comparison that also kind of distinguishes IMPUTE2: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511547/