Question: is it .impute2 format equal to .gen format
gravatar for Peter Chung
3.1 years ago by
Peter Chung120
Hong Kong
Peter Chung120 wrote:

I would like to apply qctool software from .impute2 format to .bgen format. However,

qctool -g HELLO.impute2 -og HELLO.bgen

Error comes out:

!! Error (genfile::BadArgumentError): In argument(s) filetype_hint="guess", inferred type = "" to function genfile::SNPDataSource::create(): Unrecognised file type..

So I should transform the .impute2 format to .gen format then to .bgen format.

But I checked on the file that the format of impute2 is same as gen format.

So anyone know how to apply the qctool package to the .impute2 file

qctool imputation impute2 • 1.7k views
ADD COMMENTlink modified 8 months ago by Kevin Blighe63k • written 3.1 years ago by Peter Chung120

IMPUTE2 should produce output in GEN format. How have you run IMPUTE?, i.e., how was HELLO.impute2 produced?

ADD REPLYlink written 8 months ago by Kevin Blighe63k
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