Are imputed individuals included back into the reference panel?

odelaneau / GLIMPSE

Low Coverage Calling of Genotypes

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Are imputed individuals included back into the reference panel? #199

Closed sahwa closed 7 months ago

sahwa commented 7 months ago

Hi quick question - if you run GLIMPSE v1.1.1 with a reference panel, are the target individuals who have been imputed then included back into the reference panel? i.e. does the inclusion of different target individuals affect how the other target individuals are imputed?

Thanks,

Sam.

srubinacci commented 7 months ago

Hi,

yes, that is a main difference between GLIMPSE2 and GLIMPSE1.1.1. For reference panel only imputation, GLIMPSE2 should be the method of choice.

Best,

Simone