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Revision as of 06:17, 26 April 2011
, 06:17, 26 April 2011→Shoud I use MaCH or minimac?
The imputation quality of both approaches is comparable.
The imputation quality of both approaches is comparable.
If you are carrying out only an one-time imputation, using a reference panel with <200 haplotypes and focusing only on autosomes - then go with MaCH.
If you are carrying out only an one-time imputation, using a reference panel with <200 haplotypes and focusing only on autosomes - then go with MaCH. If you are using a large reference panel, planning to re-impute your data as new reference panels become available or interested in X-chromosome imputation - then minimac is the right choice for you.
Since the current 1000G reference set includes 500+ European haplotypes, you'll probably be better off using [[minimac]].
[[Image:Imputation_approaches.png|border]]
== Getting Started ==
== Getting Started ==
